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Although liquid-liquid phase separation (LLPS) has been extensively studied in various cellular and organismal contexts, the link between functional influence of a genetic mutation and LLPS with respect to human diseases is poorly understood. A recent article by Mensah et al. looks at a rare genetic disease to identify a frameshift mutation, which triggered aberrant phase separation and nucleolar dysregulation, linking genetic variants to a dysregulation of biomolecular condensates. [ABSTRACT FROM AUTHOR]

The interplay between the early collapse of the unfolded state and the formation of the secondary structure has been the subject of extensive research in protein chemistry. In this study, we used the intestinal fatty acid binding protein (IFABP), a small model protein with predominately /i-sheet structure, to study the early events, including the early chain collapse and the formation of the secondary structure. We used a combination of fluorescence correlation spectroscopy and far-UV circular dichroism (CD) to understand how these early processes influence the late folding events like the stabilization of the secondary structure and aggregation. Acid-induced unfolded LFABP was found to collapse in the presence of low concentrations of added salt and aggregate at higher concentrations. Both the formation of the collapsed state and aggregation were conveniently probed by fluorescence correlation spectroscopy, a sensitive fluorescence technique with single-molecule resolution. In contrast, the formation of the secondary structure was monitored by far-UV CD. The results suggested that backbone hydrogen bond formation, not oniy the overall hydrophobicity of IFABP, may play crucial roles in the early collapse. Two mutant proteins positioned at a crucial nucleating site, namely, G80V and L64G, although being opposite in their overall hydrophobicity, collapsed relatively rapidly compared to the wild-type protein. The interconnection among the early collapse, the formation of the secondary structure, and aggregation was similar for these two mutants. Another mutant, G44V, which was identical in its overall hydrophobicity to G80V but situated in a region distant from the hydrophobic core, was found to be very different from G80V and L64G. [ABSTRACT FROM AUTHOR]

Protein aggregation and phase separation appear to play important roles in diseases like amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD), but the interplay between different participating molecular events-which may facilitate or inhibit one another-can be difficult to study by conventional ensemble methods. In a recent study, Kevin Rhine and co-workers make use of point mutations to demonstrate the contrasting behaviour of condensates arising from Glycine and Arginine FUS mutants using single molecules fluorescence measurements. [ABSTRACT FROM AUTHOR]

What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. [ABSTRACT FROM AUTHOR]

The simplest dynamic model for an unfolded protein is a statistical coil that continually undergoes substantial conformational fluctuations. A growing number of studies indicate that the unfolded protein is not a simple random coil but rather forms transient structures. We have directly measured the rate of conformational fluctuations of unfolded intestinal fatty acid binding protein (131 aa, 15 kDa) by using fluorescence self-quenching in combination with fluorescence correlation spectroscopy. The conformational fluctuations in this state have an apparent relaxation time, m, of 1.6 μsec in 3 M guanidine-HCI at pH 7 and 20°C. The value of ΤR increases with increasing solution viscosity, suggesting a diffusive process. In the molten globule state at pH 2, 1k is 2.5 ,.tsec, increasing further with the formation of salt-induced secondary structure. These measurements, which should be widely applicable to other systems, can provide important information about the still incompletely understood conformational properties of unfolded proteins and the mechanism of protein folding. [ABSTRACT FROM AUTHOR]

The interaction of submicellar concentrations of sodium dodecyl sulfate (SDS) with horse heart cytochrome c has been found to stabilize two spectroscopically distinct partially folded intermediates at pH 7. The first intermediate is formed by the interaction of SDS with native cytochrome c, and this intermediate retains the majority of the secondary structure while the tertiary structure of the protein is lost. The unfolding of this intermediate with urea leads to the formation of a second intermediate, which is also formed on refolding of the unfolded protein (unfolded by urea) by SDS. The second intermediate retains about 50% of the native secondary structure with no tertiary structure of the protein. The second intermediate was found to be absent at low pH. While induction of helical structure of a protein by SDS in the native condition has been reported earlier, this is possibly the first report of the refolding of a protein in a strongly denaturing condition (in the presence of 10 M urea). The relative contributions of the hydrophobic and the electrostatic interactions of the surfactants with cytochrome c have been determined from the formation of the molten globule species from the acid-induced unfolded protein in the presence of SDS or lauryl maltoside. [ABSTRACT FROM AUTHOR]

Interaction of lauryl maltoside (LM) surfactant with bovine heart cytochrome c oxidase (CcO) has been studied by NMR techniques. Detailed 2-D 1H and 13C NMR techniques were used to assign the NMR signals of the surfactant nuclei. Paramagnetic dipolar shift of the surfactant 13C NMR signals were used to identify the atoms close to the enzyme. The diamagnetic carbon monoxide complex of CcO did not cause any shift in the surfactant NMR spectra suggesting that the paramagnetic centres of the native CcO cause the shifts by dipolar interactions. The results showed that the polar head groups of the surfactant comprised of two maltoside rings are more affected, while the hydrophobic tail groups did not show any significant change on binding of the surfactant to the enzyme. This indicated that surfactant head groups possibly bind to the enzyme surface and the hydrophobic tail of the surfactant forms micelles and remains away from the enzyme. Based on the results, we propose that the membrane bound enzyme is possibly stabilised in aqueous solution by association with the micelles of the neutral surfactant so that the polar heads of the micelles bind to the polar surface of the enzyme. These micelles might form a ‘belt like’ structure around the enzyme helping it to remain monodispersed in the active form. [Copyright &y& Elsevier]

Presents the findings of a study on the effect of temperature and pH on the structural and conformational stability of horseradish peroxidase isoenzyme c (HRPc). Use of detailed circular dichroism and tryptophan fluorescence in the experiment; Thermal unfolding of HRP; Change in tryptophan fluorescence of HRPc with temperature.

It is now established that a protein can switch between multiple conformations to enable altered functions. Several pathogens including SARS COV2 utilize context-dependent conformational switches of particular proteins to invade host membrane to establish infections. In this perspective, we first discuss the understanding of the conformational switch of a protein towards the productive infections as a dark side of nature. Next, the unexplored binary combination of the sequences of SARS COV2 spike protein and the similarity with diverse pathogen derived proteins have been discussed to obtain novel molecular insights into the process of infection. Sannigrahi et al. discuss conformational switching that allows proteins to alter their conformation, aiding in pathogenesis by enabling cellular entry of viruses and bacterial toxins. Focussing on fusion domain of the Spike glycoprotein of SARS COV2 virus, they identify similar "switching sequences" present in diverse pathogen derived proteins. [ABSTRACT FROM AUTHOR]

Aggregation of the prion protein has strong implications in the human prion disease. Sup35p is a yeast prion, and has been used as a model protein to study the disease mechanism. We have studied the pattern of Sup35p aggregation inside live yeast cells under stress, by using confocal microscopy, fluorescence activated cell sorting and western blotting. Heat shock proteins are a family of proteins that are produced by yeast cells in response to exposure to stressful conditions. Many of the proteins behave as chaperones to combat stress-induced protein misfolding and aggregation. In spite of this, yeast also produce small molecules called osmolytes during stress. In our work, we tried to find the reason as to why yeast produce osmolytes and showed that the osmolytes are paramount to ameliorate the long-term effects of lethal stress in Saccharomyces cerevisiae, either in the presence or absence of Hsp104p. [ABSTRACT FROM AUTHOR]

Accumulating evidence suggests that amyloid plaqueassociated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils are closely associated with lipids under physiological conditions; however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of amyloid Beta 40 (Aβ-40) with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation, we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40-myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils. [ABSTRACT FROM AUTHOR]

The misfolding and mutation of Cu/Zn superoxide dismutase (SOD1) is commonly associated with amyotrophic lateral sclerosis (ALS). SOD1 can accumulate within stress granules (SGs), a type of membraneless organelle, which is believed to form via liquid–liquid phase separation (LLPS). Using wild‐type, metal‐deficient, and different ALS disease mutants of SOD1 and computer simulations, we report here that the absence of Zn leads to structural disorder within two loop regions of SOD1, triggering SOD1 LLPS and amyloid formation. The addition of exogenous Zn to either metal‐free SOD1 or to the severe ALS mutation I113T leads to the stabilization of the loops and impairs SOD1 LLPS and aggregation. Moreover, partial Zn‐mediated inhibition of LLPS was observed for another severe ALS mutant, G85R, which shows perturbed Zn‐binding. By contrast, the ALS mutant G37R, which shows reduced Cu‐binding, does not undergo LLPS. In addition, SOD1 condensates induced by Zn‐depletion exhibit greater cellular toxicity than aggregates formed by prolonged incubation under aggregating conditions. Overall, our work establishes a role for Zn‐dependent modulation of SOD1 conformation and LLPS properties that may contribute to amyloid formation. Synopsis: The formation of membraneless organelles, such as stress granules (SGs), is believed to occur through the process of liquid–liquid phase separation (LLPS). The amyotrophic lateral sclerosis (ALS) disease‐associated protein SOD1 is known to accumulate within SGs, but if it itself undergoes LLPS, and if this affects amyloid formation, is not well‐studied. The apo form of SOD1 undergoes LLPS.SOD1 LLPS and subsequent aggregation are regulated by a conformational transition between a disordered and a relatively compact folded state.The metal cofactor Zn prevents SOD1 LLPS via a conformational transition.SOD1 condensates show greater cytotoxicity than aggregates. [ABSTRACT FROM AUTHOR]

Conventional drug development strategies typically use pocket in protein structures as drug-target sites. They overlook the plausible effects of protein evolvability and resistant mutations on protein structure which in turn may impair protein-drug interaction. In this study, we used an integrated evolution and structure guided strategy to develop potential evolutionary-escape resistant therapeutics using receptor binding domain (RBD) of SARS-CoV-2 spike-protein/S-protein as a model. Deploying an ensemble of sequence space exploratory tools including co-evolutionary analysis and deep mutational scans we provide a quantitative insight into the evolutionarily constrained subspace of the RBD sequence-space. Guided by molecular simulation and structure network analysis we highlight regions inside the RBD, which are critical for providing structural integrity and conformational flexibility. Using fuzzy C-means clustering we combined evolutionary and structural features of RBD and identified a critical region. Subsequently, we used computational drug screening using a library of 1615 small molecules and identified one lead molecule, which is expected to target the identified region, critical for evolvability and structural stability of RBD. This integrated evolution-structure guided strategy to develop evolutionary-escape resistant lead molecules have potential general applications beyond SARS-CoV-2. [ABSTRACT FROM AUTHOR]

MPT63, a secreted protein of unknown function that isspecificto Mycobacterium tuberculosisand a potential drugtarget, contains four Tryptophan (Trp/W) residues located at positions26, 48, 82, and 129 in the amino acid sequence. All of the four Trpresidues have been optically resolved by simple inexpensive phosphorescencespectroscopy at 77 K. The protein architecture provides a delicatemicro-environment and location of Trp residues giving rise to fourdifferent (0,0) bands in the phosphorescence spectra. Calculationof intra Trp energy transfer (ET) efficiency, accessible surface area(ASA) of Trp residues, and environment of Trp in the wild-type (WT)and the mutant W26F [where, Trp 26 is replaced by phenyl alanine (Phe/F)]reveal: ET1(W82) > ET1(W48) > ET1(W129) > ET1(W26), where ET1isthe lowest(π–π*) triplet state energy of Trp. The (0,0) bandobserved at 421.6 nm assigned for Trp 26 is found to be the longestwavelength (0,0) band so far reported in the literature. Fluorescencein WT and W26F is dominated by buried or partially exposed Trp residuesindicated by time-resolved spectra. Circular Dichroism (CD) studiesand the time-resolved anisotropy measurement confirm the unalteredsecondary and tertiary structure of the mutant compared to that ofthe WT. Excitation energy dependent phosphorescence spectra suggestthat the intensity of the different (0,0) bands could be tuned andTyrosine (Tyr/Y) residue is silent in emission . Optical resolutionof all the Trp residues will help understand the role of each Trpresidue in the folding/unfolding mechanism and in the interactionwith other systems. [ABSTRACT FROM AUTHOR]

An insight into the conformation and dynamics of unfolded and early intermediate states of a protein is essential to understand the mechanism of its aggregation and to design potent inhibitor molecules. Fluorescence correlation spectroscopy has been used to study the effects of several model protein stabilizers on the conformation of the unfolded state and early folding dynamics of tetramethyl rhodamine-labeled cytochrome c from Saccharomyces cerevisiae at single molecular resolution. Special attention has been given to arginine, which is a widely used stabilizer for improving refolding yield of different proteins. The value of the hydrodynamic radius (rH) obtained by analyzing the intensity fluctuations of the diffusing molecules has been found to increase in a two-state manner as the protein is unfolded by urea. The results further show that the presence of arginine and other protein stabilizers favors a relatively structured conformation of the unfolded states (rH of 29 Å) over an extended one (rH of 40 Å), which forms in their absence. Also, the time constant of a kinetic component (τR) of about 30 µs has been observed by analyzing the correlation functions, which represents formation of a collapsed state. This time constant varies with urea concentration representing an inverted Chevron plot that shows a roll-over behavior in the absence of arginine. To the best of our knowledge, this is one of the first applications of fluorescence correlation spectroscopy to study direct folding kinetics of a protein. [ABSTRACT FROM AUTHOR]

Arginine has been used extensively as an excipient in the formulation development of protein- based biopharmaceuticals. We investigate the role of arginine in suppressing protein aggregation and its mechanism by using bovine serum albumin as a model system. By using sedimentation velocity and other analytical techniques, we show that the use of arginine inhibits temperature-induced aggregation of the protein. We use fluorescence correlation spectroscopy and other spectroscopic techniques to show that arginine inhibits accumulation of partially folded intermediates, potentially involved in the aggregation process. The hydrodynamic radii of the protein in its native, unfolded, and intermediate states have been determined using fluorescence correlation spectroscopy at single-molecule resolution. A possible mechanism of the effects of arginine and its role as an aggregation suppressor has been discussed. [ABSTRACT FROM AUTHOR]

The fibrillation pathway of alpha-Synuclein, the causative protein of Parkinson's disease, encompasses transient, heterogeneous oligomeric forms whose structural understanding and link to toxicity are not yet understood. We report that the addition of the physiologically-available small molecule heme at a sub-stoichiometric ratio to either monomeric or aggregated α-Syn, targets a His50 residue critical for fibril-formation and stabilizes the structurally-heterogeneous populations of aggregates into a minimally-toxic oligomeric state. Cryo-EM 3D reconstruction revealed a 'mace'-shaped structure of this monodisperse population of oligomers, which is comparable to a solid-state NMR Greek key-like motif (where the core residues are arranged in parallel in-register sheets with a Greek key topology at the C terminus) that forms the fundamental unit/kernel of protofilaments. Further structural analyses suggest that heme binding induces a distortion in the Greek key-like architecture of the mace oligomers, which impairs their further appending into protofilaments and fibrils. Additionally, our study reports a novel mechanism of prevention as well as reclamation of amyloid fibril formation by blocking an inter-protofilament His50 residue using a small molecule. Chakraborty et al. present biophysical and structural insights into fibril-forming oligomers of alpha-synuclein stabilized by heme. They show that heme targets the His50 residue of the oligomers and locks the protein into a different conformation which leads to non-toxic, non-fibrillating oligomer formation, therefore addressing a very important issue in the field of structure of transient oligomers. [ABSTRACT FROM AUTHOR]

Aggregation of Cu–Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, amyotrophic lateral sclerosis (ALS). Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not correlated with disease pathophysiology. Here, we use multiple mutational variants of SOD1 to show that the absence of Zn, and not Cu, significantly impacts membrane attachment of SOD1 through two loop regions facilitating aggregation driven by lipid-induced conformational changes. These loop regions influence both the primary (through Cu intake) and the gain of function (through aggregation) of SOD1 presumably through a shared conformational landscape. Combining experimental and theoretical frameworks using representative ALS disease mutants, we develop a ‘co-factor derived membrane association model’ wherein mutational stress closer to the Zn (but not to the Cu) pocket is responsible for membrane association-mediated toxic aggregation and survival time scale after ALS diagnosis. [ABSTRACT FROM AUTHOR]

Binding interactions of KMP-11 with the IL choline dihydrogen phosphate (CDHP) solvent have been explored from multispectroscopic studies in conjunction with docking and molecular dynamics simulations. The protein KMP-11, a vaccine candidate against 'Leishmaniasis', does not contain any tryptophan (Trp) in its WT sequence. For this study, two single site Trp mutant proteins Y5W and Y89W of KMP -11 have been generated as Trp used as biomarker by the aid of intrinsic fluorescence. In the former mutant (Y5W) Trp is inserted in the vicinity of the N-terminal, while in the later (Y89W), the same residue is disposed near the C-terminal of the protein. The binding interactions of CDHP with both the mutant proteins have been explored from UV–Vis, steady state and time resolved fluorescence spectroscopic studies. The bimolecular quenching rate constant (k q) at various temperatures, as obtained from fluorescence spectroscopic studies suggest definite but weak binding interactions between the mutant proteins and CDHP IL solvent. This result is further corroborated from the near and far - UV Circular Dichroism (CD) spectra. The possible binding sites of CDHP in the vicinity of WT and mutant proteins and the corresponding binding forces have been predicted from the molecular docking studies. The results of MD simulation further portend minimal or no unfolding in the secondary structures of the WT and the mutant proteins upon addition of CDHP molecule. We believe that this in-depth study featuring the interaction of KMP-11 with IL CDHP will enlighten the fundamental understanding towards the development of improved protein based vaccines in general and KMP-11 guided vaccines in particular for the prevention of VL. Unlabelled Image • Binding interactions of KMP-11 and its Trp mutants with ionic liquid (IL) CDHP • Interactions explored by both multi-spectroscopic and theoretical studies. • Quenching of fluorescence and the thermodynamic parameters were estimated. • Changes in protein conformation suggested by near and far CD measurements. • Enlightening the development of protein based vaccine against visceral Leishmaniasis [ABSTRACT FROM AUTHOR]

A crucial contribution to the heterogeneity of the conformational landscape of a protein comes from the way an intermediate relates to another intermediate state in its journey from the unfolded to folded or misfolded form. Unfortunately, it is extremely hard to decode this relatedness in a quantifiable manner. Here, we developed an application of statistical cluster analyses to explore the conformational heterogeneity of a metalloenzyme, human cytosolic copper–zinc superoxide dismutase (SOD1), using the inputs from infrared spectroscopy. This study provides a quantifiable picture of how conformational information at one particular site (for example, the copper-binding pocket) is related to the information at the second site (for example, the zinc-binding pocket), and how this relatedness is transferred to the global conformational information of the protein. The distance outputs were used to quantitatively generate a network capturing the folding sub-stages of SOD1. [ABSTRACT FROM AUTHOR]

Parkinson's disease (PD), closely associated with the misfolding and aggregation of the neuronal protein α-synuclein (A-Syn), is a neurodegenerative disorder with no cure to date. Here, we show that the commercially available, inexpensive, aminoglycoside antibiotic kanamycin effectively inhibits both lipid-induced and solution-phase aggregation of A-Syn in vitro, pointing towards the prospective repurposing of kanamycin as a potential anti-PD drug. [ABSTRACT FROM AUTHOR]

A novel rhodamine-tryptamine conjugate-based fluorescent and chromogenic chemosensor (RTS) for detection of Hg2+ present in water was reported. After gradual addition of Hg2+ in aqueous methanol solution of RTS, a strong orange fluorescence and deep-pink coloration were observed. The probe showed high selectivity towards Hg2+ compared to other competitive metal ions. The 1:1 binding stoichiometry between RTS and Hg2+ was established by Job's plot analysis and mass spectroscopy. Initial studies showed that the synthesized probe RTS possessed fair non-toxicity and effectively passed through cell walls of model cell systems, viz., human neuroblastoma (SHSY5Y) cells and cervical cells (HeLa) to detect intercellular Hg2+ ions, signifying its utility in biological system. The limit of detection (LOD) was found to be 2.1 nM or 0.42 ppb by fluorescence titration. Additionally, the potential relevance of synthesized chemosensor for detecting Hg2+ ions in environmental water samples has been demonstrated.ᅟ [ABSTRACT FROM AUTHOR]

Background: Malignant diseases have become a threat for health care system. A panoply of biological processes is involved as the cause of these diseases. In order to unveil the mechanistic details of these diseased states, we analyzed protein families relevant to these diseases. Results: Our present study pivots around four apparently unrelated cancer types among which two are commonly occurring viz. Prostate Cancer, Breast Cancer and two relatively less frequent viz. Acute Lymphoblastic Leukemia and Lymphoma. Eight protein families were found to have implications for these cancer types. Our results strikingly reveal that some of the proteins with implications in the cancerous cellular states were showing the structural organization disparate from the signature of the family it constitutes. The sequences were further mapped onto respective structures and compared with the entropic profile. The structures reveal that entropic scores were able to reveal the inherent structural bias of these proteins with quantitative precision, otherwise unseen from other analysis. Subsequently, the betweenness centrality scoring of each residue from the structure network models was resorted to explore the changes in dependencies on residue owing to structural disorder. Conclusion: These observations help to obtain the mechanistic changes resulting from the structural orchestration of protein structures. Finally, the hydropathy indexes were obtained to validate the sequence space observations using Shannon entropy and in-turn establishing the compatibility. [ABSTRACT FROM AUTHOR]

Background/Aims: The conformation, folding and lipid binding properties of the intestinal fatty acid binding proteins (IFABP) have been extensively investigated. In contrast, the functional aspects of these proteins are not understood and matter of debates. In this study, we aim to address the deleterious effects of FA overload on cellular components, particularly mitochondria; and how IFABP helps in combating this stress by restoring the mitochondrial dynamics. Methods: In the present study the functional aspect of IFABP under conditions of lipid stress was studied by a string of extensive in-cell studies; flow cytometry by fluorescence-activated cell sorting (FACS), confocal imaging, western blotting and quantitative real time PCR. We deployed ectopic expression of IFABP in rescuing cells under the condition of lipid stress. Again in order to unveil the mechanistic insights of functional traits, we arrayed extensive computational approaches by means of studying centrality calculations along with protein-protein association and ligand induced cluster dissociation. While addressing its functional importance, we used FCS and in-silico computational analyses, to show the structural distribution and the underlying mechanism of IFABP's action. Results: Ectopic expression of IFABP in HeLa cells has been found to rescue mitochondrial morphological dynamics and restore membrane potential, partially preventing apoptotic damage induced by the increased FAs. These findings have been further validated in the functionally relevant intestinal Caco-2 cells, where the native expression of IFABP protects mitochondrial morphology from abrogation induced by FA overload. However, this native level expression is insufficient to protect against apoptotic cell death, which is rescued, at least partially in cells overexpressing IFABP. In addition, shRNA mediated IFABP knockdown in Caco-2 cells compromises mitochondrial dynamics and switches on intrinsic apoptotic pathways under FA-induced metabolic stress. Conclusion: To summarize, the present study implicates functional significance of IFABP in controlling ligand-induced damage in mitochondrial dynamics and apoptosis. [ABSTRACT FROM AUTHOR]

A novel pyrrole fused coumarin based simple and practicable molecular probe has been synthesized under metal free green conditions which can recognize copper (II) in acetonitrile solvent. The synthesized probe displayed fluorescence quenching through selective binding with Cu 2+ over other competitive metal ions. Job’s plot, 1 H NMR titration and Mass spectral study revealed that the most abundant species formed when metal to ligand ratio was 1:1. The limit of detection (LOD) for Cu 2+ was found to be 11.3 nM or 2 ppb which is significantly lower than the maximum contaminant level (1.3 ppm of Cu), according to United State Environmental Protection Agency (USEPA). The fluorescent sensor was highly cell permeable and illustrated fluorescence ‘Turn-Off’ in presence of Cu 2+ ions in fluorescent imaging of human cervical cancer (HeLa) cell. [ABSTRACT FROM AUTHOR]

Genetic switches frequently include DNA loops secured by proteins. Recent studies of the lambda bacteriophage repressor (CI), showed that this arrangement in which the protein links two sets of three operators separated by approximately 2.3 kbp, optimizes both the stability and dynamics of DNA loops, compared to an arrangement with just two sets of two operators. Because adjacent dimers interact pairwise, we hypothesized that the odd number of operators in each set of the lambda regulatory system might have evolved to allow for semi-specific, pair-wise interactions that add stability to the loop while maintaining it dynamic. More generally, additional CI dimers may bind non-specifically to flanking DNA sequences making the genetic switch more sensitive to CI concentration. Here, we tested this hypothesis using spectroscopic and imaging approaches to study the binding of the lambda repressor (CI) dimer protein to DNA fragments. For fragments with only one operator and a short flanking sequence, fluorescence correlation spectroscopy measurements clearly indicated the presence of two distinct DNA-CI complexes; one is thought to have a non-specifically bound CI dimer on the flanking sequence. Scanning force micrographs of CI bound to DNA with all six operators revealed wild-type or mutant proteins bound at operator positions. The number of bound, wild-type proteins increased with CI concentration and was larger than expected for strictly specific binding to operators. In contrast, a mutant that fails to oligomerize beyond a dimer, D197G, only bound to operators. These data are evidence that CI cooperativity promotes oligomerization that extends from operator sites to influence the thermodynamics and kinetics of CI-mediated looping. [ABSTRACT FROM AUTHOR]

The sole existence of a t-bone-shaped naphthalimide derivative [2-(2-aminoethyl)-1 H-benzo[de]isoquinoline-1,3(2 H)dione] (NAP), which gives rise to a photoinduced electron transfer (PET) mechanism, has been established using a combination of experimental and theoretical studies. In parallel an in vitro-in cell PET mechanism has also been shown. To understand the photophysics of NAP, solvent studies have been carried out in different solvents. In addition, theoretical calculations have been conducted to explain the spectroscopic properties through optimized structures. A 'turn off' PET mechanism has also been observed in the presence of specific metal ions, namely, Cr3+, Fe3+ and Hg2+ among a series of metal ions. Theoretical studies reveal that NAP-Cr3+, NAP-Fe3+ and NAP-Hg2+ have their HOMO energy states lying in between a HOMO-LUMO energy state of the t-bone-type NAP molecule. On the contrary, the HOMO state of the other metal ion-NAP conjugate (NAP-M n+) does not lie in between the HOMO-LUMO energy gap of the t-bone-type NAP molecule. Coupled with in vitro studies, in cell investigations reveal an enhancement of fluorescence intensity of NAP upon cytosolic metal sensing. Furthermore, a very high cell viability of NAP treated cells as tested by MTT assay and a fast permeation of the said compound as revealed by flow cytometry suggest NAP to be a potential candidate in metal sensing and bioimaging applications. [ABSTRACT FROM AUTHOR]

Fluorescent metal nanoclusters have generated considerable excitement in nanobiotechnology, particularly in the applications of biolabeling, targeted delivery, and biological sensing. The present work is an experimental and computational study that aims to understand the effects of protein environment on the synthesis and electronic properties of gold nanoclusters. MPT63, a drug target of Mycobacterium tuberculosis, was used as the template protein to synthesize, for the first time, gold nanoclusters at a low micromolar concentration of the protein. Two single cysteine mutants of MPT63, namely, MPT63Gly20Cys (mutant I) and MPT63Gly40Cys (mutant II) were employed for this study. The experimental results show that cysteine residues positioned in two different regions of the protein induce varying electronic states of the nanoclusters depending on the surrounding amino acids. A mixture of five-atom and eight-atom clusters was generated for each mutant, and the former was found to be predominant in both cases. Computational studies, including density functional theory (DFT), frontier molecular orbital (FMO), and natural bond orbital (NBO) calculations, validated the experimental observations. The as-prepared protein-stabilized nanoclusters were found to have applications in the imaging of live cells. [ABSTRACT FROM AUTHOR]

KMP-11 is a small protein that is believed to control the overall bilayer pressure of the Leishmania parasite. Recent results have suggested that membrane binding and the presence of cholesterol affect the efficacy of Leishmanial infection, in which KMP-11 plays an important role. Nevertheless, there exists no systematic study of membrane interaction with KMP-11 either in the absence or presence of cholesterol. In this article, we investigated the interaction between KMP-11 and phospholipid membranes using an unsaturated (PC 18:1; 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)) and saturated (PC 12:0; 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC)) lipid as membrane mimics. Additionally, we studied the effect of cholesterol on the protein-membrane interaction. Steady-state as well as time-resolved fluorescence spectroscopy, isothermal titration calorimetry (ITC), and ζ-potential measurements were used for the determination of the binding constants for the wild-type (WT) and single-site tryptophan mutants. Single-site tryptophan mutants were designed to make sure that the tryptophan residues sample different surface exposures in different mutants. In the absence of cholesterol, the membrane-binding affinities of the partially exposed and buried tryptophan mutants (Y5W and Y48W, respectively) were found to be greater than those of the WT protein. In the presence of cholesterol, the binding constants of the WT and Y48W mutant were found to decrease with an increase in cholesterol concentration. This was in contrast to that in the Y5W and F77W mutants, in which the binding constants increased on adding cholesterol. The present study highlights the interplay among the conformational architecture of a protein, its interaction with the membrane, and membrane composition in modulating the survival of a Leishmania parasite inside host macrophages. [ABSTRACT FROM AUTHOR]

To understand how a protein folds and behaves inside living cells, the effects of synthetic crowding media on protein folding, function, stability, and association have been studied in detail. Because the effect of excluded volume is more prominent in an extended state than in the native protein, a majority of these studies have been conducted in the unfolded state of different model proteins. Here, we have used fluorescence correlation spectroscopy (FCS) and other biophysical methods to investigate the effect of crowding agents Ficoll70 and Dextran70 on the nativelike state of cytochrome c from yeast. Yeast cytochrome c (y-cytc) contains a substantial expanded state in its native folded condition, which is present in equilibrium with a compact conformer in aqueous buffer. We have found that the crowding medium affects the native state equilibrium between compact and expanded states, shifting its population toward the compact conformer. As a result, the peroxidase activity of y-cytc decreases. Urea-induced protein stability measurements show that the compaction destabilizes the protein due to charge repulsions between similar charged clusters. Interestingly, the time constant of conformational fluctuations between the compact and expanded conformers has been found to increase in the crowded milieu, suggesting a crucial role of the solution microviscosity. [ABSTRACT FROM AUTHOR]

Although the primary function of cytochrome c (cyt c) is electron transfer, the protein caries out an additional secondary function involving its interaction with membrane cardiolipin (CDL), its peroxidase activity, and the initiation of apoptosis. Whereas the primary function of cyt c is essentially conserved, its secondary function varies depending on the source of the protein. We report here a detailed experimental and computational study, which aims to understand, at the molecular level, the difference in the secondary functions of cyt c obtained from horse heart (mammalian) and Saccharomyces cerevisiae (yeast). The conformational landscape of cyt c has been found to be heterogeneous, consisting of an equilibrium between the compact and extended conformers as well as the oligomeric species. Because the determination of relative populations of these conformers is difficult to obtain by ensemble measurements, we used fluorescence correlation spectroscopy (FCS), a method that offers single-molecule resolution. The population of different species is found to depend on multiple factors, including the protein source, the presence of CDL and urea, and their concentrations. The complex interplay between the conformational distribution and oligomerization plays a crucial role in the variation of the pre-apoptotic regulation of cyt c observed from different sources. Finally, computational studies reveal that the variation in the charge distribution at the surface and the charge reversal sites may be the key determinant of the conformational stability of cyt c. [ABSTRACT FROM AUTHOR]

The aggregation of α-synuclein(A-syn) has been implicatedin the pathogenesis of Parkinson’s disease (PD). Although theearly events of aggregation and not the matured amyloid fibrils arebelieved to be responsible for the toxicity, it has been difficultto probe the formation of early oligomers experimentally. We studiedthe effect of Fe3O4nanoparticle (NP) in theearly stage of aggregation of A-syn using fluorescence correlationspectroscopy (FCS) and laser scanning microscopy. The binding betweenthe monomeric protein and NPs was also studied using FCS at single-moleculeresolution. Our data showed that the addition of bare Fe3O4NPs accelerated the rate of early aggregation, andit did not bind the monomeric A-syn. In contrast, l-lysine(Lys)-coated Fe3O4NPs showed strong bindingwith the monomeric A-syn, inhibiting the early events of aggregation.Lys-coated Fe3O4NPs showed significantly lesscell toxicity compared with bare Fe3O4NPs andcan be explored as a possible strategy to develop therapeutic applicationagainst PD. To the best of our knowledge, this report is the firstexample of using a small molecule to attenuate the early (and arguablythe most relevant in terms of PD pathogenesis) events of A-syn aggregation. [ABSTRACT FROM AUTHOR]

Trehalose-6-phosphate phosphatase (TPP) catalyzes the final step in the biosynthesis of the anti-stress sugar trehalose. An 82 kDa TPP enzyme was isolated from Candida utilis with 61% yield and 43-fold purification. The protein sequence, determined by N-terminal sequencing and MALDI-TOF analysis, showed significant homology with known TPP sequences from related organisms. The full length gene sequence of TPP of C. utilis was identified using rapid amplification of cDNA ends-PCR reaction (RACE-PCR). The gene was cloned and expressed in Escherichia coli BL21. Recombinant TPP enzyme was isolated using affinity chromatography. CD spectroscopy and steady-state fluorescence revealed that the structural and conformational aspects were identical in both native and recombinant forms. The biochemical properties of the two forms were also similar. Km was determined to be ~0.8 mM. Optimum temperature and pH were found to be 30 °C and 8.5, respectively. Activity was dependent on the presence of divalent cations and inhibited by metal chelators. Methylation-mediated regulation of TPP enzyme and its effect on the overall survival of the organism under stress were investigated. The results indicated that enhancement of TPP activity by methylation at the Cysteine residues increased resistance of Candida cells against thermal stress. This work involves extensive investigations toward understanding the physico-chemical properties of the first TPP enzyme from any yeast strain. The mechanism by which methylation regulates its activity has also been studied. A correlation between regulation of trehalose synthesis and survivability of the organism under thermal stress was established. J. Cell. Physiol. 229: 1245-1255, 2014. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Protein aggregation is believed to occur through the formation of misfolded conformations. It is expected that, in order to minimize aggregation, an effective small molecule chaperone would destabilize these intermediates. To study the mechanism of a chemical chaperone, we have designed a series of mutant proteins in which a tryptophan residue experiences different local environments and solvent exposures. We show that these mutants correspond to a series of conformationally altered proteins with varying degree of misfolding stress and aggregation propensities. Using arginine as a model small molecule, we show that a combination of unfolded state contraction and denaturant like properties results in selective targeting and destabilization of the partially folded proteins. In comparison, the effect of arginine towards the folded like control mutant, which is not aggregation prone, is significantly less. Other small molecules, lacking either of the above two properties, do not offer any specificity towards the misfolded proteins. [ABSTRACT FROM AUTHOR]

The presence of magnetic nanoparticles (NPs) in physiological systems induces toxicity through its effects on mitochondrial function and reactive oxygen species (ROS) imbalance. Magnetic NP induced cytotoxicity has been elaborately evaluated for impending threats, however, a detailed investigation is lacking. It is shown that the interaction of Fe3O4 NPs with cytochrome c can lead to different events based on the NPs to protein ratio, the solution conditions, and the type of surface protection. At low NPs concentration, rapid binding and subsequent electron transfer are the preferred events while at higher concentration slow oxidative modification of the protein is initiated. The slow event of protein modification yields conformational disorientation, loss of stability, and formation of amyloid-like structures with cytochrome c. The possibility that the NP induced oxidative stress and age can work in concert to compromise different aspects of cellular quality control processes is discussed. Suitable surface modifications of the NPs inhibit their direct binding to the protein molecules and minimize NP induced toxicity. [ABSTRACT FROM AUTHOR]

Abstract: Trehalose and sucrose, two important anti-stress non-reducing natural disaccharides, are catabolized by two enzymes, namely trehalase and invertase respectively. In this study, a 175kDa enzyme protein active against both substrates was purified from wild type Candida utilis and characterized in detail. Substrate specificity assay and activity staining revealed the enzyme to be specific for both sucrose and trehalose. The ratio between trehalase and invertase activity was found to be constant at 1:3.5 throughout the entire study. Almost 40-fold purification and 30% yield for both activities were achieved at the final step of purification. The presence of common enzyme inhibitors, thermal and pH stress had analogous effects on its trehalase and invertase activity. K m values for two activities were similar while V max and K cat also differed by a factor of 3.5. Competition plot for both substrates revealed the two activities to be occurring at the single active site. N-terminal sequencing and MALDI-TOF data analysis revealed higher similarity of the purified protein to previously known neutral trehalases. While earlier workers mentioned independent purification of neutral trehalase or invertase from different sources, the present study reports the purification of a single protein showing dual activity. [Copyright &y& Elsevier]

Viperin, an antiviral protein, has been shown to contain a CX3CX2C motif, which is conserved in the radical S-adenosyl-methionine (SAM) enzyme family. A triple mutant which replaces these three cysteines with alanines has been shown to have severe deficiency in antiviral activity. Since the crystal structure of Viperin is not available, we have used a combination of computational methods including multi-template homology modeling and molecular dynamics simulation to develop a low-resolution predicted structure. The results show that Viperin is an α -β protein containing iron-sulfur cluster at the center pocket. The calculations suggest that the removal of iron-sulfur cluster would lead to collapse of the protein tertiary structure. To verify these predictions, we have prepared, expressed and purified four mutant proteins. In three mutants individual cysteine residues were replaced by alanine residues while in the fourth all the cysteines were replaced by alanines. Conformational analyses using circular dichroism and steady state fluorescence spectroscopy indicate that the mutant proteins are partially unfolded, conformationally unstable and aggregation prone. The lack of conformational stability of the mutant proteins may have direct relevance to the absence of their antiviral activity. [ABSTRACT FROM AUTHOR]

Superoxide dismutase (SOD) is the primary enzyme of the cellular antioxidant defense cascade. Misfolding, concomitant oligomerization, and higher order aggregation of human cytosolic SOD are linked to amyotrophic lateral sclerosis (ALS). Although, with two metal ion cofactors SOD1 is extremely robust, the de-metallated apo form is intrinsically disordered. Since the rise of oxygen-based metabolism and antioxidant defense systems are evolutionary coupled, SOD is an interesting protein with a deep evolutionary history. We deployed statistical analysis of sequence space to decode evolutionarily co-varying residues in this protein. These were validated by applying graph theoretical modelling to understand the impact of the presence of metal ion co-factors in dictating the disordered (apo) to hidden disordered (wild-type SOD1) transition. Contact maps were generated for different variants, and the selected significant residues were mapped on separate structure networks. Sequence space analysis coupled with structure networks helped us to map the evolutionarily coupled co-varying patches in the SOD1 and its metal-depleted variants. In addition, using structure network analysis, the residues with a major impact on the internal dynamics of the protein structure were investigated. Our results reveal that the bulk of these evolutionarily co-varying residues are localized in the loop regions and positioned differentially depending upon the metal residence and concomitant steric restrictions of the loops. [ABSTRACT FROM AUTHOR]

The image shows the major findings of Goutam De, Krishnananda Chattopadhyay, and coworkers, who studied the interaction between iron oxide nanoparticles and cytochrome c, as reported on page 683. The triangle at the top left shows the binding of the protein onto the surface of the bare particles forming amyloid fibrils (transmission electron microscopy image is shown in the background). Appropriate surface modification inhibits protein binding and amyloid formation (shown in the triangle at the bottom right). [ABSTRACT FROM AUTHOR]