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Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.

Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The stem-cement interface in total hip replacement experiences fretting wear following debonding under cyclical physiological loading. However, the influence of protein concentration on the biotribological properties of this interface has not been well taken into consideration. In the present study, a series of fretting frictional tests were performed using polished Ti6Al4V and bone cement, lubricated by bovine serum albumin solutions of different concentrations (5%, 30%, and 75%). Surface characterizations of Ti6Al4V pins were conducted by optical interferometer, scanning electron microscope, and Raman spectroscopy. The results show that the friction coefficient decreases with the increase of protein concentration, although the difference is not significant. In addition, bovine serum albumin is adsorbed onto Ti6Al4V surface, forming a protective film to prevent the metal substrate from wear. The elemental and spectroscopic analyses of the film confirm the presence of protein molecules adsorbed on Ti6Al4V surface, with a thickness of 2.5 μm. It is indicated from this study that fretting wear at the stem-cement interface can be postponed by promotion of protein adsorption on the metal surface.

Mutations in drug targets can alter the therapeutic effects of drugs. Therefore, evaluating the effects of single-nucleotide polymorphisms (SNPs) on drug-target binding is of significant interest. This study focuses on the analysis of the structural and energy properties of SNPs in successful drug targets by using the data derived from HapMap and the Therapeutic Target Database. The results show the following: (i) Drug targets undergo strong purifying selection, and the majority (92.4%) of the SNPs are located far from the drug-binding sites (>12 Å). (ii) For SNPs near the drug-binding pocket (≤12 Å), nearly half of the drugs are weakly affected by the SNPs, and only a few drugs are significantly affected by the target mutations. These results have direct implications for population-based drug therapy and for chemical treatment of genetic diseases as well.

New strategies for target identification are urgently needed to tackle the current productivity challenges in drug discovery. By examining successful human drug targets, it can be seen that approximately 50% are associated with genetic disorders. Further analysis shows that these successfully targeted genes share some common evolutionary features, which strongly suggests that evolutionary information can help identify drug targets with the greatest potential for therapeutic development., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

The origin and evolution of modern biochemistry remain a mystery despite advances in evolutionary bioinformatics. Here, we use a structural census in nearly 1,000 genomes and a molecular clock of folds to define a timeline of appearance of protein families linked to single-domain enzymes. The timeline sorts out enzymatic recruitment, validates patterns in metabolic history, and reveals that the most ancient reaction of aerobic metabolism involved the synthesis of pyridoxal 5'-phosphate or pyridoxal and appeared 2.9 Gyr ago. The oxygen source for this primordial reaction was probably Mn catalase, which appeared at the same time and could have generated oxygen as a side product of hydrogen peroxide detoxification. Finally, evolutionary analysis of transferred groups and metabolite fragments revealed that oxidized sulfur did not participate in metabolism until the rise of oxygen. The evolutionary patterns we uncover in molecules and chemistries provide strong support for the coevolution of biochemistry and geochemistry., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Objective: To explore an effective method of Dermatophagoides pteronyssinus protein extraction suitable for two-dimensional electrophoresis (2-DE) analysis., Methods: The extracts of Dermatophagoides pteronyssinus were prepared with Coca's solution, lysis buffer of 2-DE, and Trizol reagent, respectively. Bicinchoninic acid (BCA) assay was used to determine the total protein concentration of the samples. The efficiency of different protein extraction methods were evaluated with 2-DE analysis., Results: The concentrations of extracted protein by methods of Coca's solution, lysis buffer, and Trizol reagent were 0.63 g/L, 0.90 g/L, and 0.80 g/L, respectively. The 2-DE analysis results showed that some protein spots in low molecular weight (LMW) range could be detected with the Coca's solution method. With the lysis buffer of 2-DE method, more protein spots in LMW range could be detected, while the medium molecular weight (MMW) protein spots were absent. Several MMW protein spots (174-178 kD and 133 kD) and more LMW protein spots were detected with Trizol reagent method., Conclusions: Among Coca's solution, lysis buffer of 2-DE, and Trizol reagent, the concentration of extracted protein of Dermatophagoides pteronyssinus by lysis buffer of 2-DE is the highest. However, most protein components of Dermatophagoides pteronyssinus purified mite bodies can be extracted by Trizol reagent, which may generally reflect the whole profile of Dermatophagoides pteronyssinus allergens.

Protein folding experiments demonstrate that the folding behaviors of many proteins can be roughly classified into two types: two-state kinetics and multi-state kinetics. Although the two types of protein folding kinetics have been observed for a long time, what determines the folding type of a protein is still largely unclear. The present work performed a comparative study based on a dataset of 43 two-state and 42 multi-state folders at different levels of proteins' intrinsic properties from the simplest sequence length to native structure topology. The results show that protein's amino acids composition and the long-range interaction-based topological complexity rather than secondary structure contents are the major determinants of protein folding type. Furthermore, a sequence-based folding type prediction achieved an accuracy of more than 80%. These findings implicate that there is no clear boundary between secondary and tertiary structure formation during the protein folding process and support the existence of a continuum of folding mechanism between the two ends of hierarchic and nucleation folding scenarios.

It is well known that due to the degeneracy of genetic code, most of the silent substitutions appear in the third codon position, so the mutation frequency of the third codon position is much higher than that of the first two positions. However, it remains unknown whether the directionality of point mutation in three codon positions is similar or not. In this paper, through analyzing 15 sets of orthologous genes, it is revealed that most of the substitution types are significantly different between any two codon positions, especially between the 2nd and the 3rd phases. Furthermore, the average frequencies of each type of substitution calculated from the fifteen sets of orthologous genes are similar to those identified in single nucleotide polymorphisms (SNPs) of human and mouse genome. The present analyses suggest that the nucleotide substitution in protein-coding sequences is not only context-dependent (so called neighboring-nucleotide effects), but also phase-dependent, which is of significance to improving the prevalent nucleotide-evolution models.

Inferring the protein architecture chronology is one of central topics in origin of life study and has been given much attention. Based on an amino acid evolutionary model that late amino acids were bio-synthesized prior to early counterparts, we addressed the issue by examining the structures of amino acid synthases. Despite the limited structural information on amino acid synthases, our deduction revealed that alpha/beta was the oldest protein class, which is in good agreement with the prior fold-usage-based conclusion.

Background: Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping., Results: By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super ligands (shared by three or more folds) from others., Conclusion: These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products.

Discovering the mechanism of protein folding, in molecular biology, is a great challenge. A key step to this end is to find factors that correlate with protein folding rates. Over the past few years, many empirical parameters, such as contact order, long-range order, total contact distance, secondary structure contents, have been developed to reflect the correlation between folding rates and protein tertiary or secondary structures. However, the correlation between proteins' folding rates and their amino acid compositions has not been explored. In the present work, we examined systematically the correlation between proteins' folding rates and their amino acid compositions for two-state and multistate folders and found that different amino acids contributed differently to the folding progress. The relation between the amino acids' molecular weight and degeneracy and the folding rates was examined, and the role of hydrophobicity in the protein folding process was also inspected. As a consequence, a new indicator called composition index was derived, which takes no structure factors into account and is merely determined by the amino acid composition of a protein. Such an indicator is found to be highly correlated with the protein's folding rate (r > 0.7). From the results of this work, three points of concluding remarks are evident. (1) Two-state folders and multistate folders have different rate-determining amino acids. (2) The main determining information of a protein's folding rate is largely reflected in its amino acid composition. (3) Composition index may be the best predictor for an ab initio protein folding rate prediction directly from protein sequence from the standpoint of practical application., ((c) 2006 Wiley-Liss, Inc.)

Oxidative stress and excessive redox metals have been implicated in the pathogenesis of Alzheimer's disease (AD), which leads to the tentative employment of radical scavengers and metal chelators in clinical therapy of AD. The preliminary successes of both therapy strategies inspire us to propose that better clinical effects can be expected for a compound combining radical-scavenging potential with metal-protein-attenuating ability. Based on theoretical investigation, we indicate that two novel metal chelators (1-(benzimidazole-2-ylmethyl)-1,4,7-triazacyclononane and 1,4-bis(benzimidazole-2-ylmethyl)-1,4,7-triazacyclonone), especially the latter, are promising to fulfill this new strategy.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tips.2010.07.003 Byline: Hong-Yu Zhang (1), Ling-Ling Chen (2), Xue-Juan Li (1), Jian Zhang (3) Abstract: Conceptual innovations are needed to address the challenge of 'more investments, fewer drugs' in the pharmaceutical industry. Since the publication of The Origin of Species by Charles Darwin 150 years ago, evolution has been a central concept in biology. In this article, we show that evolutionary concepts are also helpful to streamline the drug-discovery pipeline through facilitating the discovery of targets and drug candidates. Furthermore, the antioxidant paradox can be addressed by an evolutionary methodology. Through examining the evolved biological roles of natural polyphenols (which dominate current antioxidant drug discovery), we reveal that polyphenols (particularly flavonoids) are not evolved for scavenging free radicals. This finding provides new clues to understanding why the strong in vitro antioxidant activities of polyphenols cannot be translated into in vivo effects. Polyphenols have evolved a superior ability to bind various proteins, so we also argue that they are good starting points for multi-target drugs. Author Affiliation: (1) National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China (2) State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China (3) Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, P. R. China

Gamma‐proteobacteria Xanthomonas spp. cause at least 350 different plant diseases among important agricultural crops, which result in serious yield losses. Xanthomonas spp. rely mainly on the type III secretion system (T3SS) to infect their hosts and induce a hypersensitive response in nonhosts. HrpG, the master regulator of the T3SS, plays the dominant role in bacterial virulence. In this study, we used chromatin immunoprecipitation followed by sequencing (ChIP‐seq) and tandem affinity purification (TAP) to systematically characterize the HrpG regulon and HrpG interacting proteins in vivo. We obtained 186 candidate HrpG downstream genes from the ChIP‐seq analysis, which represented the genomic‐wide regulon spectrum. A consensus HrpG‐binding motif was obtained and three T3SS genes, hpa2, hrcU, and hrpE, were confirmed to be directly transcriptionally activated by HrpG in the inducing medium. A total of 273 putative HrpG interacting proteins were identified from the TAP data and the DNA‐binding histone‐like HU protein of Xanthomonas campestris pv. campestris (HUxcc) was proved to be involved in bacterial virulence by increasing the complexity and intelligence of the bacterial signalling pathways in the T3SS. [ABSTRACT FROM AUTHOR]

Hypertrophic scars (HTS) and keloids are challenging problems. Their pathogenesis results from an overproduction of fibroblasts and excessive deposition of collagen. Studies suggest a possible anti-scarring effect of basic fibroblast growth factor (bFGF) during wound healing, but the precise mechanisms of bFGF are still unclear. In view of this, we investigated the therapeutic effects of bFGF on HTS animal model as well as human scar fibroblasts (HSF) model. We show that bFGF promoted wound healing and reduced the area of flattened non-pathological scars in rat skin wounds and HTS in the rabbit ear. We provide evidence of a new therapeutic strategy: bFGF administration for the treatment of HTS. The scar elevation index (SEI) and epidermal thickness index (ETI) was also significantly reduced. Histological reveal that bFGF exhibited significant amelioration of the collagen tissue. bFGF regulated extracellular matrix (ECM) synthesis and degradation via interference in the collagen distribution, the α-smooth muscle actin (α-SMA) and transforming growth factor-1 (TGF-β1) expression. In addition, bFGF reduced scarring and promoted wound healing by inhibiting TGFβ1/SMAD-dependent pathway. The levels of fibronectin (FN), tissue inhibitor of metalloproteinase-1 (TIMP-1) collagen I, and collagen III were evidently decreased, and matrix metalloproteinase-1 (MMP-1) and apoptosis cells were markedly increased. These results suggest that bFGF possesses favorable therapeutic effects on hypertrophic scars in vitro and in vivo, which may be an effective cure for human hypertrophic scars. [ABSTRACT FROM AUTHOR]

The stem-cement interface in total hip replacement experiences fretting wear following debonding under cyclical physiological loading. However, the influence of protein concentration on the biotribological properties of this interface has not been well taken into consideration. In the present study, a series of fretting frictional tests were performed using polished Ti6Al4V and bone cement, lubricated by bovine serum albumin solutions of different concentrations (5%, 30%, and 75%). Surface characterizations of Ti6Al4V pins were conducted by optical interferometer, scanning electron microscope, and Raman spectroscopy. The results show that the friction coefficient decreases with the increase of protein concentration, although the difference is not significant. In addition, bovine serum albumin is adsorbed onto Ti6Al4V surface, forming a protective film to prevent the metal substrate from wear. The elemental and spectroscopic analyses of the film confirm the presence of protein molecules adsorbed on Ti6Al4V surface, with a thickness of 2.5 μm. It is indicated from this study that fretting wear at the stem-cement interface can be postponed by promotion of protein adsorption on the metal surface. [ABSTRACT FROM AUTHOR]

Abstract: To compare the thermostabilities of human and chicken normal cellular prion proteins (HuPrPC and CkPrPC), molecular dynamics (MD) simulations were performed for both proteins at an ensemble level (10 parallel simulations at 400K and 5 parallel simulations at 300K as a control). It is found that the thermostability of HuPrPC is comparable with that of CkPrPC, which implicates that the non-occurrence of prion diseases in non-mammals cannot be completely attributed to the thermodynamic properties of non-mammalian PrPC. [Copyright &y& Elsevier]

Autophagy is involved in the development and/or progression of many diseases, including myocardial ischemia/reperfusion (I/R). In this study, we hypothesized a protective role of basic fibroblast growth factor (bFGF) both in vivo and in vitro and demonstrated that excessive autophagy and ubiquitinated protein accumulation is involved in the myocardial I/R model. Our results showed that bFGF improved heart function recovery and increased the survival of cardiomyocytes in myocardial I/R model. The protective effect of bFGF is related to the inhibition of LC3II levels. Additionally, bFGF enhances the clearance of Ub by p62 and increases the survival of H9C2 cells. Moreover, silencing of p62 partially blocks the clearance of Ub and abolishes the anti-apoptosis effect of bFGF. An shRNA against the autophagic machinery Atg7 increased the survival of H9C2 cells co-treated with bFGF and rapamycin. bFGF activates the downstream signaling of the PI3K/Akt/mTOR pathway. These results indicate that the role of bFGF in myocardial I/R recovery is related to the inhibition of excessive autophagy and increased ubiquitinated protein clearance via the activation of PI3K/Akt/mTOR signaling. Overall, our study suggests a new direction for bFGF drug development for heart disease and identifies protein signaling pathways involved in bFGF action. [ABSTRACT FROM AUTHOR]

Abstract: Although the context dependence of nucleotide mutation has been supported by accumulating theoretical and experimental evidence, whether this effect can be extended to amino acid mutation remains obscure. As the amino acid doublets (20×20) are much more diverse than their nucleotide counterparts (4×4), any attempt to address the neighboring-site effects of amino acid mutation was frustrated by deficient amino acid mutation data. Based on the recently revealed 599,745 mutation sites in 45,137 orthologous proteins, we provide solid evidence for the first time to support the existence of neighboring-site effects in amino acid mutation, which is significantly important to improving the prevalent protein-evolution models. [Copyright &y& Elsevier]

Hypertrophic scars (HTS) and keloids are challenging problems. Their pathogenesis results from an overproduction of fibroblasts and excessive deposition of collagen. Studies suggest a possible anti-scarring effect of basic fibroblast growth factor (bFGF) during wound healing, but the precise mechanisms of bFGF are still unclear. In view of this, we investigated the therapeutic effects of bFGF on HTS animal model as well as human scar fibroblasts (HSF) model. We show that bFGF promoted wound healing and reduced the area of flattened non-pathological scars in rat skin wounds and HTS in the rabbit ear. We provide evidence of a new therapeutic strategy: bFGF administration for the treatment of HTS. The scar elevation index (SEI) and epidermal thickness index (ETI) was also significantly reduced. Histological reveal that bFGF exhibited significant amelioration of the collagen tissue. bFGF regulated extracellular matrix (ECM) synthesis and degradation via interference in the collagen distribution, the α-smooth muscle actin (α-SMA) and transforming growth factor-1 (TGF-β1) expression. In addition, bFGF reduced scarring and promoted wound healing by inhibiting TGFβ1/SMAD-dependent pathway. The levels of fibronectin (FN), tissue inhibitor of metalloproteinase-1 (TIMP-1) collagen I, and collagen III were evidently decreased, and matrix metalloproteinase-1 (MMP-1) and apoptosis cells were markedly increased. These results suggest that bFGF possesses favorable therapeutic effects on hypertrophic scars in vitro and in vivo, which may be an effective cure for human hypertrophic scars. [ABSTRACT FROM AUTHOR]

Abstract: Tracing the characters of very ancient proteins represents one of the biggest challenges in the study of origin of life. Although there are no primitive protein fossils remaining, the characters of very ancient proteins can be traced by molecular fossils embedded in modern proteins. In this paper, first the prior findings in this area are outlined and then a new strategy is proposed to address the intriguing issue. It is interesting to find that various molecular fossils and different protein datasets lead to similar conclusions on the features of very ancient proteins, which can be summarized as follows: (i) the architectures of very ancient proteins belong to the following folds: P-loop containing nucleoside triphosphate hydrolases (c.37), TIM beta/alpha-barrel (c.1), NAD(P)-binding Rossmann-fold domains (c.2), Ferredoxin-like (d.58), Flavodoxin-like (c.23) and Ribonuclease H-like motif (c.55); (ii) the functions of very ancient proteins are related to the metabolisms of purine, pyrimidine, porphyrin, chlorophyll and carbohydrates; (iii) a certain part of very ancient proteins need cofactors (such as ATP, NADH or NADPH) to work normally. [Copyright &y& Elsevier]

Abstract: The protein WrbA from Escherichia coli is the founding member of a class of novel multimeric flavodoxin-like proteins implicated in defense against oxidative stress. Although, WrbA is predicted to share the twisted α/β open-sheet fold of the flavodoxins and to bind flavin mononucleotide (FMN) as its physiological cofactor, the binding is much weaker in comparison with flavodoxin (the binding constants are ∼2μM for WrbA and ∼1nM for flavodoxin). To elucidate the different FMN-binding behaviors of WrbA and flavodoxin, we modeled the WrbA structure and examined its interactions with FMN by docking experiments, and then compared them with those at the flavodoxin active site. The results provide a rationale for the reduced cofactor affinity displayed by WrbA relative to flavodoxin. [Copyright &y& Elsevier]