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Glycosylation is one of the most common post-translational modifications (PTMs), which provides a large proteome diversity. Previous work on glycosylation of globular proteins has revealed remarkable effects of glycosylation on protein function, altering the folding stability and structure and/or altering the protein surface which affects their binding characteristics. Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of large proteins are also frequently glycosylated, yet how glycosylation affects their function remains to be elucidated. An important open question is, does glycosylation affect IDP structure or binding characteristics or both? In this work, we particularly address the structural effects of O-linked glycosylation by investigating glycosylated and unglycosylated forms of two different IDPs, tau174-183 and human islet amyloid polypeptide (hIAPP), by all-atom explicit solvent simulations. We simulate these IDPs in aqueous solution for O-linked glycosylated and unglycosylated forms by employing two modern all-atom force fields for which glycan parameters are also available. We find that O-linked glycosylation only has a modest effect on equilibrium structural ensembles of IDPs, for the cases studied here, which suggests that the functional role of glycosylation may be primarily exerted by modulation of the protein binding characteristics rather than structure. [ABSTRACT FROM AUTHOR]

We used single molecule force spectroscopy to measure the force required to remove single-stranded DNA (ssDNA) homopolymers from single-walled carbon nanotubes (SWCNTs) deposited on methyl-terminated self-assembled monolayers (SAMs). The peeling forces obtained from these experiments are bimodal in distribution. The cluster of low forces corresponds to peeling from the SAM surface, while the cluster of high forces corresponds to peeling from the SWCNTs. Using a simple equilibrium model of the single molecule peeling process, we calculated the free energy of binding per nucleotide. We found that the free energy of ssDNA binding to hydrophobic SAMs decreases as poly(A) > poly(G) ≈ poly(T) > poly(C) (16.9 ± 0.1; 9.7 ± 0.1; 9.5 ± 0.1; 8.7 ± 0.1 kBT, per nucleotide). The free energy of ssDNA binding to SWCNT adsorbed on this SAM also decreases in the same order poly(A) > poly(G) > poly(T) > poly(C), but its magnitude is significantly greater than that of DNA—SAM binding energy (38.1 ± 0.2; 33.9 ± 0.1; 23.3 ± 0.1; 17.1 ± 0.1 kBT, per nucleotide). An unexpected finding is that binding strength of ssDNA to the curved SWCNTs is much greater than to flat graphite, which also has a different ranking (poly(T) > poly(A) > poly(G) > poly(C); 11.3 ± 0.8, 9.9 ± 0.5, 8.3 ± 0.2, and 7.5 ± 0.8 kBT, respectively, per nucleotide). Replica-exchange molecular dynamics simulations show that ssDNA binds preferentially to the curved SWCNT surface, leading us to conclude that the differences in ssDNA binding between graphite and nanotubes arise from the spontaneous curvature of ssDNA. [ABSTRACT FROM AUTHOR]

Intrinsically disordered proteins (IDPs), which playkey rolesin cell signaling and regulation, do not display specific tertiarystructure when isolated in solution. Instead, they dynamically explorean ensemble of unfolded configurations, adopting more stable, orderedstructures only after binding to their ligands. Whether ligands induceIDP structural changes upon binding or simply bind to pre-existingconformers that are populated within the IDP’s structural ensembleis not well understood. Molecular simulations can provide informationwith the spatiotemporal resolution necessary to resolve these issues.Here, we report on the conformational ensemble of a 15-residue wild-typep53 fragment from the TAD domain and its mutant (TAD-P27L) obtainedby replica exchange molecular dynamics simulation using an optimized(fully atomistic, explicit solvent) protein model and the experimentalvalidation of the simulation results. We use a clustering method basedon structural similarity to identify conformer states populated bythe peptides in solution from the simulated ensemble. We show thatp53 populates solution structures that strongly resemble the ligand(MDM2)-bound structure, but at the same time, the conformational free-energylandscape is relatively flat in the absence of the ligand. [ABSTRACT FROM AUTHOR]

Amyloid aggregates are characteristic of many serious diseases such as Alzheimer's disease, Parkinson's, and type 2 diabetes and commonly involve intrinsically disordered proteins (IDPs), those that populate an ensemble of conformations rather than a single folded structure. Human islet amyloid polypeptide (hIAPP or amylin) is an amyloidogenic IDP implicated in pancreatic β-cell death during the pathogenesis of type 2 diabetes. The target of amylin's toxic activity is thought to be the cell's lipid membrane, which may also act as a catalyst for aggregation. Since amylin is intrinsically disordered, differing environments can have a large impact on its equilibrium conformational ensemble. We apply atomistic molecular dynamics simulations on multiple systems containing a full-length amylin monomer and a lipid bilayer to study the changes induced by the membrane. We observe stabilized helical conformations structurally similar to those determined by NMR experiments conducted in similar environments. We also find that bilayers of different compositions result in greatly different equilibrium ensembles of amylin. Finally, we discuss how a mixed bilayer containing zwitterionic and anionic lipid headgroups can allow for greater preference toward conformations which are adsorbed below the membrane surface through rearrangement of lipids for more favorable protein-lipid interactions. [ABSTRACT FROM AUTHOR]

We use all-atom molecular simulationwith explicit solvent to studythe properties of selected intrinsically disordered proteins and unfoldedstates of foldable proteins, which include chain dimensions and shape,secondary structure propensity, solvent accessible surface area, andcontact formation. We find that the qualitative scaling behavior ofthe chains matches expectations from theory under ambient conditions.In particular, unfolded globular proteins tend to be more collapsedunder the same conditions than charged disordered sequences of thesame length. However, inclusion of explicit solvent in addition naturallycaptures temperature-dependent solvation effects, which results inan initial collapse of the chains as temperature is increased, inqualitative agreement with experiment. There is a universal originto the collapse, revealed in the change of hydration of individualresidues as a function of temperature: namely, that the initial collapseis driven by unfavorable solvation free energy of individual residues,which in turn has a strong temperature dependence. We also observethat in unfolded globular proteins, increased temperature also initiallyfavors formation of native-like (rather than non-native-like) structure.Our results help to establish how sequence encodes the degree of intrinsicdisorder or order as well as its response to changes in environmentalconditions. [ABSTRACT FROM AUTHOR]

Thecholesterol recognition/interaction amino acid consensus (CRAC)motif is a primary structure pattern used to identify regions thatmay be responsible for preferential cholesterol binding in many proteins.The leukotoxin LtxA, which is produced by a pathogenic bacterium,contains two CRAC seqences, only one of which is responsible for cholesterolbinding, and the binding is required for cytotoxicity. The factors,in addition to the CRAC definition, that may be responsible for cholesterol-bindingfunctionality and atomistic interactions between the CRAC region andcholesterol are as yet unknown. This study uses molecular dynamicssimulations to identify structural characteristics and specific interactionsof the two LtxA CRAC peptides with both pure phospholipid and binarycholesterol–phospholipid bilayers. We have identified changesin the secondary structure of these peptides that occur upon cholesterolbinding, which are not seen when it is associated with a cholesterol-devoidmembrane, and which show salient coupling of structural disorder andfunction. Additionally, the central tyrosine residue of the CRAC motifwas found to play a significant role in cholesterol binding, thoughresidues outside of the CRAC motif also influence membrane interactionsand functionality of the CRAC region. [ABSTRACT FROM AUTHOR]

Replicaexchange molecular dynamics simulations are performed onthe protein complex pKID–KIX to understand the effects of macromolecularcrowding on coupled folding and binding events. A structure-basedprotein model at the residue level is adopted for the two proteinsto include intramolecular conformational flexibility, while crowdingmacromolecules are represented as spherical particles. The interactionsbetween crowders and protein residues can be either purely repulsiveor a combination of short-range repulsion and intermediate-range attraction.Consistent with previous studies on rigid-body protein binding inthe presence of spherical crowders, we find that the complex formationis stabilized by repulsive protein–crowder interactions anddestabilized by sufficiently strong attractive protein–crowderinteractions. Competition between stabilizing repulsive and destabilizingattractive interactions is quantitatively captured by a previous theoreticalmodel developed for describing the change in the binding free energyof rigid proteins in a crowded environment. We find that protein flexibilityhas little effect on the thermodynamics of the pKID–KIX binding(with respect to bulk) for repulsive and weakly attractive protein–crowderinteractions. For strong protein–crowder attractive interactions,the destabilizing effect due to crowding is attenuated by proteinflexibility. Interestingly, the mechanism of coupled folding and bindingobserved in bulk remains unchanged under highly crowded conditionsover a broad range of protein–crowder interaction strengths.Also, strong protein–crowder attractive interactions can significantlystabilize intermediate states involving partial contact between pKIDand KIX domains. [ABSTRACT FROM AUTHOR]

Human islet amyloid polypeptide (hIAPP),a 37-residue protein cosecretedwith insulin by β-cells in the pancreas, is known to form amyloidfibrils in type II diabetes patients. This fibril formation is alsoassociated with β-cell death. However, rat IAPP (rIAPP) doesnot aggregate into fibrils, nor is it associated with β-celltoxicity. Determining solutionproperties of hIAPP experimentally is difficult because it aggregatesquickly. Our study uses molecular dynamics simulation to explore andcompare in-solution characteristics of hIAPP and rIAPP, as well astwo single-point hIAPP mutants, hIAPP I26P and hIAPP S20G, which exhibitobserved differences from hIAPP in aggregation propensities. We findthat all four polypeptide monomers sample structured states in solution.More importantly, differences in the helicity over residues 7–16may play an important role in early aggregation, although this regionis outside of commonly assumed amyloidogenic region 20–29.The long-range contacts, though unexpected of IDPs, cause variationin sampled conformations among four polypeptides within same aminoacid sequence. Our results also yield evidence that previously determinedstructures bound to micelles are also transiently sampled in the solutionstate. In particular, similarities found in region 8–17 togetherwith the helical differences that we observe in region 7–16lead us to suggest that the region 7–16 is potentially responsiblefor amyloidogenic behavior of amylin peptides. Our results also providesupport for the proposed mechanism of fibril formation based on experimentallyobserved transient helices in amyloidogenic peptides. [ABSTRACT FROM AUTHOR]

The single-stranded DNA to single-walled carbon nanotube(SWCNT)hybrid continues to attract significant interest as an exemplary biologicalmolecule–nanomaterial conjugate. In addition to their manybiomedical uses, such as in vivo sensing and delivery of molecularcargo, DNA-SWCNT hybrids enable the sorting of SWCNTs according totheir chirality. Current experimental methods have fallen short ofidentifying the actual structural ensemble of DNA adsorbed onto SWCNTsthat enables and controls several of these phenomena. Molecular dynamics(MD) simulation has been a useful tool for studying the structureof these hybrid molecules. In recent studies, using replica exchangeMD (REMD) simulation we have shown that novel secondary structuresemerge and that these structures are DNA-sequence and SWCNT-type dependent.Here, we use REMD to investigate in detail the structural characteristicsof two DNA-SWCNT recognition pairs: (TAT)4-(6,5)-SWCNT,i.e., DNA sequence TATTATTATTAT bound to the (6,5)chirality SWCNT, and (CCG)2CC-(8,7)-SWCNT as well as off-recognitionpairs (TAT)4-(8,7)-SWCNT and (CCG)2CC-(6,5)-SWCNT.From a structural clustering analysis, dominant equilibrium structuresare identified and show a right-handed self-stitched motif for (TAT)4-(6,5) in contrast to a left-handed β-barrel for (CCG)2CC-(8,7). Additionally, characteristics such as DNA end-to-enddistance, solvent accessible SWCNT surface area, DNA hydrogen bondingbetween bases, and DNA dihedral distributions have been probed indetail as a function of the number of DNA strands adsorbed onto thenanotube. We find that the DNA structures adsorbed onto a nanotubeare also stabilized by significant numbers of non-Watson–Crickhydrogen bonds (intrastrand and interstrand) in addition to π–πstacking between DNA bases and nanotube surface and Watson–Crickpairs. Finally, we provide a summary of DNA structures observed forvarious DNA-SWCNT hybrids as a preliminary set of motifs that maybe involved in the functional role of these hybrids. [ABSTRACT FROM AUTHOR]

Single- and double-stranded DNA are increasingly beingpaired withsurfaces and nanoparticles for numerous applications, such as sensing,imaging, and drug delivery. Unlike the majority of DNA structuresin bulk that are stabilized by canonical Watson–Crick pairingbetween Ade-Thy and Gua-Cyt, those adsorbed on surfaces are oftenstabilized by noncanonical base pairing, quartet formation, and base–surfacestacking. Not much is known about these kinds of interactions. Tobuild an understanding of the role of non-Watson–Crick pairingon DNA behavior near surfaces, one requires basic information on DNAbase pair stacking and hydrogen-bonding interactions. All-atom molecularsimulations of DNA bases in two casesin bulk water and stronglyadsorbed on a graphite surfaceare conducted to study the relativestrengths of stacking and hydrogen bond interactions for each of the10 possible combinations of base pairs. The key information obtainedfrom these simulations is the free energy as a function of distancebetween two bases in a pair. We find that stacking interactions exertthe dominant influence on the stability of DNA base pairs in bulkwater as expected. The strength of stability for these stacking interactionsis found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade> Gua-Thy> Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy >Cyt-Cyt. On theother hand, mutual interactions of surface-adsorbed base pairs arestabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt> Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua >Cyt-Cyt > Ade-Cyt> Thy-Thy > Gua-Thy. Interestingly, several non-Watson–Crickbase pairings, which are commonly ignored, have similar stabilizationfree energies due to interbase hydrogen bonding as Watson–Crickpairs. This clearly highlights the importance of non-Watson–Crickbase pairing in the development of secondary structures of oligonucleotidesnear surfaces. [ABSTRACT FROM AUTHOR]

The DNA-single-walled carbon nanotube (SWCNT) hybrid molecule has attracted signfficant attention recently for its ability to disperse and sort SWCNTs according to their chirality. Key for utilizing their unique properties is an understanding of the structure of DNA adsorbed on the SWCNT surface, which we study here using molecular simulations. Using replica exchange molecular dynamics (REMD), we explore equilibrium structures formed by single strands of 12-mer oligonucleotides, of varying sequence, adsorbed on a (6,5)-SWCNT. We find a consistent motif in which the DNA strand forms a right-handed helical wrap around the SWCNT, stabilized by "stitches" (hydrogen bonding between distant bases) to itself. Variability among equilibrium populations of DNA self-stitched structures was observed and shown to be directly influenced by DNA sequence and composition. Competition between conformational entropy and hydrogen bonding between bases is predicted to be responsible for the formation of random versus stitched configurations. [ABSTRACT FROM AUTHOR]

Most binary superlattices created using DNA functionalization rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized micron-sized particles (DFPs), and employ a strategy that leverages the tunable disparity in interparticle interactions, and thus enthalpic driving forces, to open new avenues for design of binary superlattices that do not rely on the ability to tune particle size (i.e., entropic driving forces). Our strategy employs tailored blends of complementary strands of ssDNA to control interparticle interactions between micron-sized silica particles in a binary mixture to create compositionally diverse 2D lattices. We show that the particle arrangement can be further controlled by changing the stoichiometry of the binary mixture in certain cases. With this approach, we demonstrate the ability to program the particle assembly into square, pentagonal, and hexagonal lattices. In addition, different particle types can be compositionally ordered in square checkerboard and hexagonal-alternating string, honeycomb, and Kagome arrangements. [ABSTRACT FROM AUTHOR]

We report the effect of nonionic surfactants (Pluronics F127 and F88) on the melting transition of micron-sized colloids confined in two dimensions, mediated by complementary single-stranded DNA as a function of the surfactant concentration. Micron-sized silica particles were functionalized with single-stranded DNA using cyanuric chloride chemistry. The existence of covalently linked DNA on particles was confirmed by fluorescence spectroscopy. The nonionic surfactant not only plays a significant role in stabilization of particles, with minimization of nonspecific binding, but also impacts the melting temperature, which increases as a function of the nonionic surfactant concentration. These results suggest that the melting transition for DNA-mediated assembly is sensitive to commonly used additives in laboratory buffers, and that these common solution components may be exploited as a facile and independent handle for tuning the melting temperature and, thus, the assembly and possibly crystallization within these systems. [ABSTRACT FROM AUTHOR]