Protein Stability Analysis Research Articles

Pathogenic predictions of non-synonymous variants and their impacts: A computational assessment of ARHGEF6 gene

IntroductionARHGEF6, a key member and activator of RhoGTPases family that is involved in G-Protein Coupled receptor (GPCR) pathway and stimulate Rho dependent signals in the brain, and mutations in this gene can cause intellectual disability (ID) in Human. Therefore, we aimed to study the consequences of ARHGEF6 non-synonymous mutations by using advanced computational methods. MethodsClassification of the genetic mutations in ARHGEF6 gene was performed according to Ensembl Genome Database and data mining was done using ensemble tools. The functional and disease effect of missense mutations, and pathogenic characteristics of amino acid substitutions of ARHGEF6 were analyzed using eleven diversified computational tools and servers. ResultsOverall, 47 ARHGEF6 non-synonymous (NS) variants were predicted to be deleterious by SIFT, Polyphen2 and PROVEAN scores. Above that, SNPs&GO and PhD SNP were further graded 21 customarily pathogenic NS-variants. Protein stability analysis resulted in the significant change in terms of ΔΔG of most identified NS-variants, except K609I. Seven variants were analyzed to be located on most potential domain RhoGEF/DH, whereas the remaining 14 were distributed on CH, SH3, PH and BP domains. Furthermore, pathogenic effects of mutations on protein was presented with different parameters using MutPred2 and PROJECT HOPE. Additionally, STRING network data predicted GIT2 and PARVB as most interacted partners of ARHGEF6. ConclusionThese findings can be supportive of genotype-phenotype research as well as the development in pharmacogenetics studies. Finally, this study revealed a significance of computational methods to figure out highly pathogenic genomic variants linked with the structural and functional relationship of ARHGEF6 protein.

High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms

SummaryHuman cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early-phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed that helicase-like transcription factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses.

Novel mutations of ITGB2 induced leukocyte adhesion defect type 1

Objective: To investigate the pathogenic mechanism of two novel ITGB2 mutations in leukocyte adhesion defect type 1 (LAD1). Methods: The clinical history and blood sample of an 11 years old patient admitted to Affiliated Hospital of Qingdao University in August 2014 were collected. Expression of CD18 (encoded by ITGB2) was analyzed by flow cytometry. Novel ITGB2 mutations were identified by next-generation sequencing technology and confirmed by Sanger sequencing. The functional effect of ITGB2 mutations was detected by PolyPhen2. Expression vectors of both wild type and mutant ITGB2 were constructed and transfected into mammalian cells for analysis of protein stability and subcellular location. Results: The symptoms of the patient (recurrent infections, lowered alveolar ridge and hypodontia) supported the diagnosis of LAD1. Expression of CD18 on the leukocytes was significantly decreased (0.2%) compared with the control samples from the parents (paternal: 99.0%; maternal: 99.1%). The patient was identified to be compound heterozygous for ITBG2 c.954del G (novel mutation) and c.1802C>A (paternal originated). ITGB2 c.954 del G was confirmed to be a harmful frameshift mutation; ITGB2 c.1802C>A was also predicted to be harmful. In terms of protein stability. There was no significant difference between mutant D18 and wild type. However, subcellular location analysis showed the mutant D18 could not locate on cell membrane. Conclusion: The compound heterozygous of ITGB2 mutations (c.954del G and c.1802C>A) decreases the expression and impairs the location of CD18 on leukocytes, which leads to LAD1.

Analysis of Mitochondrial Protein Synthesis: De Novo Translation, Steady-State Levels, and Assembled OXPHOS Complexes.

Mitochondria are multifunctional organelles with their own genome and protein synthesis machinery. The 13 proteins encoded by mitochondrial DNA (mtDNA) are core subunits of the oxidative phosphorylation (OXPHOS) system producing the majority of cellular ATP. Yet most mitochondrial proteins are encoded by nuclear genes, synthesized by cytosolic ribosomes, and imported into mitochondria. Therefore, disturbances in cytosolic proteostasis have consequences on the gene expression and synthesis of mtDNA-encoded proteins and overall on mitochondrial function. Internal and environmental factors such as mutations, aging, oxidative stress, and toxic agents can affect the translation and the stability of mitochondrial proteins and lead to OXPHOS dysfunction. Here, methods for analysis of mitochondrial translation rate and protein stability using radioactive and non-radioactive technique as well as the methods for studying steady-state levels and assembly of OXPHOS complexes are described. © 2018 by John Wiley & Sons, Inc.

PO-138 Dimethyl fumarate modulation of antioxidant response in cancer cells: therapeutic applications

IntroductionThe activity of Vav1 as a mutant oncogene in human tumours has remained questionable for decades. Although mutants of Vav1 were recently identified in human cancers of various origins, the functional activity of these mutants is not fully studied. Vav1 is physiologically active as a GDP/GTP nucleotide exchange factor (GEF) in the hematopoietic system. In this study, we addressed the contribution of several cancer-identified Vav1 mutants to tumorigenic processes.Material and methodsWe introduced several amino-acid substitutions at residues identified in human lung cancer as follows: glutamic acid (position 59; calponin homology region) to lysine (E59K); aspartic acid (position 517; C1 domain) to glutamic acid (D517E); and leucine (position 801; carboxySH3) to proline (L801P). The biochemical and transforming activities of these mutants were tested following transfection into NIH3T3 cells.Results and discussionsAmong the mutants produced, E59K generated a truncated protein, which preserved its expected size once cells are incubated with MG132, a specific proteasome inhibitor. E59K, D517E and oncVav1 are active as GEF towards Rho/RacGTPases, albeit E59K exhibited the uppermost activity. This result was illustrated by Pymol, a computer software for molecular visualisation, that predicts its increased activity as a GEF. This activity is also manifested in changes in cytoskeleton organisation indicative of transformation. Analysis of protein stability using cycloheximide decay assay revealed that D517E mutant protein is more stable than the other mutants, thus explaining its increased expression and activity. Furthermore, NIH3T3 cells expressing E59K, D517E and oncVav1 mutants exhibit increased cell proliferation, elevated number of transformed foci and increased number of generated tumours in NOD/Scid mice. Of note is the fact that tumours generated by E59K exhibit the most aggressive phenotype among the mutant proteins used in this study, reminiscent of epithelial morphology.ConclusionOur results convincingly attest to the transforming potential of the Vav1 mutants, E59K and D517E, thus providing compelling evidence that Vav1 mutants can act as ‘real’ oncogenes in human cancer.

PO-135 Analysis of the transforming activity of human cancer identified Vav1 mutants prove its classification as an oncogene

Introduction The activity of Vav1 as a mutant oncogene in human tumours has remained questionable for decades. Although mutants of Vav1 were recently identified in human cancers of various origins, the functional activity of these mutants is not fully studied. Vav1 is physiologically active as a GDP/GTP nucleotide exchange factor (GEF) in the hematopoietic system. In this study, we addressed the contribution of several cancer-identified Vav1 mutants to tumorigenic processes. Material and methods We introduced several amino-acid substitutions at residues identified in human lung cancer as follows: glutamic acid (position 59; calponin homology region) to lysine (E59K); aspartic acid (position 517; C1 domain) to glutamic acid (D517E); and leucine (position 801; carboxySH3) to proline (L801P). The biochemical and transforming activities of these mutants were tested following transfection into NIH3T3 cells. Results and discussions Among the mutants produced, E59K generated a truncated protein, which preserved its expected size once cells are incubated with MG132, a specific proteasome inhibitor. E59K, D517E and oncVav1 are active as GEF towards Rho/RacGTPases, albeit E59K exhibited the uppermost activity. This result was illustrated by Pymol, a computer software for molecular visualisation, that predicts its increased activity as a GEF. This activity is also manifested in changes in cytoskeleton organisation indicative of transformation. Analysis of protein stability using cycloheximide decay assay revealed that D517E mutant protein is more stable than the other mutants, thus explaining its increased expression and activity. Furthermore, NIH3T3 cells expressing E59K, D517E and oncVav1 mutants exhibit increased cell proliferation, elevated number of transformed foci and increased number of generated tumours in NOD/Scid mice. Of note is the fact that tumours generated by E59K exhibit the most aggressive phenotype among the mutant proteins used in this study, reminiscent of epithelial morphology. Conclusion Our results convincingly attest to the transforming potential of the Vav1 mutants, E59K and D517E, thus providing compelling evidence that Vav1 mutants can act as ‘real’ oncogenes in human cancer.

Mutational analysis of epidermal and hyperproliferative type I keratins in mild and moderate psoriasis vulgaris patients: a possible role in the pathogenesis of psoriasis along with disease severity

BackgroundMutations in keratin proteins have been vastly associated with a wide array of genodermatoses; however, mutations of keratins in psoriasis have not been fully investigated. The main aim of the current research was to identify the mutation in K14, K10, K16, and K17 genes in two stages of psoriasis patients.MethodsNinety-six psoriatic skin biopsies were collected. mRNA transcript of K14, K10, K16, and K17 was prepared, amplified, and sequenced. Sanger sequences of all keratins were further validated for mutational analysis using Mutation Surveyor and Alamut Visual. Then, in silico analysis of protein stability and protein and gene expression of all keratins was performed and validated.ResultsOut of 44 mutations, about 75% of keratins are highly pathogenic and deleterious. Remaining 25% mutations are less pathogenic and tolerated in nature. In these 33 deleterious mutations were immensely found to decrease keratin protein stability. We also found a correlation between keratin and Psoriasis Area and Severity Index score which added that alteration in keratin gene in skin causes severity of psoriasis.ConclusionsWe strongly concluded that acanthosis and abnormal terminal differentiation was mainly due to the mutation in epidermal keratins. In turn, disease severity and relapsing of psoriasis are mainly due to the mutation of hyperproliferative keratins. These novel keratin mutations in psoriatic epidermis might be one of the causative factors for psoriasis.

An In silico method to study structure, function, and regulatory role alteration mediated by single-nucleotide polymorphisms in gallbladder cancer

Introduction: Gallbladder cancer (GBC) is a fatal malignancy of gallbladder and bile ductswhich shows delayed symptoms and sometimes can be asymptomatic, being fatal. Reported globally, for a very low survival rate, it suffers from the lack of early diagnostic and prognostic markers. Single nucleotide polymorphisms (SNPs) have been reported to be associated in different cancers. Methods: In this study using in silico methods, we report for the first time a combination of SNPs from the coding and noncoding region leading to alteration in GBC. Different pipelines were designed for the study of SNPs. Regulatory role alteration of Synonymous and non-coding SNPs were studied using RegulomeDB, DeepSEA analysis and funcPred. Structural alteration and energy parameters for non-synonymous SNPs were studied by Swiss-PDB, Chimera and Gromacs. Protein stability analysis was done using MutPred, mCSM and I-mutant. Results: As a result, three potential variants from the coding region rs1042838, rs11887534, and rs700519 associated with progesterone receptor, ATP binding cassette subfamily G member 8 (ABCG8), and cytochrome P450 19A1, respectively, were predicted to be potentially damaging SNPs in GBC leading to structure and function alteration. Three noncoding SNPs (rs2978974, rs4633 and rs2830) and 1 missense SNP(rs523349) were shown to be associated with damaging effect in GBC, and one of these SNPs (rs2978974) showed significant chromatin feature alteration. Conclusion: Our study strongly shows that SNPs both in the coding and noncoding region may be exploited as a combination of potential biomarkers in early diagnosis of GBC due to structure function alteration by nonsynonymous SNPs and regulatory role alteration by noncoding SNPs.

Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains.

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this mechanism may be exploited by the Hsp90-Cdc37 chaperone to recruit and protect intrinsically dynamic kinase clients from degradation. The results of this investigation are discussed and interpreted in the context of diverse experimental data, offering new insights into mechanisms of chaperone regulation and binding.

AtRAE1 is involved in degradation of ABA receptor RCAR1 and negatively regulates ABA signalling in Arabidopsis.

The phytohormone abscisic acid (ABA) plays an important role in regulating plant growth, development, and adaption to various environmental stresses. Regulatory components of ABA receptors (RCARs, also known as PYR/PYLs) sense ABA and initiate ABA signalling through inhibiting the activities of protein phosphatase 2C in Arabidopsis. However, the way in which ABA receptors are regulated is not well known. A DWD protein AtRAE1 (for RNA export factor 1 in Arabidopsis), which may act as a substrate receptor of CUL4-DDB1 E3 ligase, is an interacting partner of RCAR1/PYL9. The physical interaction between RCAR1 and AtRAE1 is confirmed in vitro and in vivo. Overexpression of AtRAE1 in Arabidopsis causes reduced sensitivity of plants to ABA, whereas suppression of AtRAE1 causes increased sensitivity to ABA. Analysis of protein stability demonstrates that RCAR1 is ubiquitinated and degraded in plant cells and AtRAE1 regulates the degradation speed of RCAR1. Our findings indicate that AtRAE1 likely participates in ABA signalling through regulating the degradation of ABA receptor RCAR1.

Distribution of CYP2C8 and CYP2C9 amino acid substitution alleles in South Indian diabetes patients: A genotypic and computational protein phenotype study

The CYP2C8 and CYP2C9 are two major isoforms of the cytochrome P450 enzyme family, which is involved in drug response, detoxification, and disease development. This study describes the differential distribution of amino acid substitution variants of CYP2C8 (*2-I269F & *3-R139K) and CYP2C9 (*2-C144R & *3-L359A) genes in 234 type 2 diabetes mellitus (T2DM) patients and 218 healthy controls from Andhra Pradesh, South India. Single locus genotype analysis has revealed that homozygous recessive genotypes of 2C8*2-TT (P≤.03), 2C9*2-TT (P≤.02), and heterozygous 2C9*3-AC (P≤.006) are seen to be increasingly present in the case group, indicating a significant level of their association with diabetes in Andhra population. The statistical significance of these recessive genotypes has persisted even under their corresponding allelic forms (P≤.01). Genotype association results were further examined by computational protein structure and stability analysis to assess the deleteriousness of the amino acid changes. The mutant CYP 2C8 and 2C9 (both *2 and *3) proteins showed structural drifts at both amino acid residue (range 0.43Å-0.77Å), and polypeptide chain levels (range 0.68Å-1.81Å) compared to their wild-type counterparts. Furthermore, the free energy value differences (range -0.915 to -1.38 Kcal/mol) between mutant and native protein structures suggests the deleterious and destabilizing potential of amino acid substitution polymorphisms of CYP genes. The present study confirms the variable distribution of CYP2C8 (*2 and *3) and CYP2C9 (*2 and *3) allelic polymorphisms among South Indian diabetic populations and further warrants the serious attention of CYP gene family, as a putative locus for disease risk assessment and therapy.

Photodegradation Pathways of Protein Disulfides: Human Growth Hormone.

Comprehensive product characterization was performed for the photodegradation of protein disulfides, representatively of human growth hormone (somatotropin; hGH), in order to provide a product database, which will be useful for the general analysis of protein stability. HGH was photo-irradiated at λ = 254 and λ > 295nm and tryptic digests were analyzed by HPLC-MS to investigate light-induced disulfide degradation pathways. A total of 60 products were detected, and structures/tentative structures were assigned to the products by MS2 and MS3 analysis. The main products were reduced Cys residues, dithiohemiacetal, thioether and disulfide scrambling products. In addition, we detected Cys degradation products such as Cys thioaldehyde, dehydroalanine (Dha), Ala, Ser semialdehyde, Ser, S-sulfocysteine, and Gly. Frequently, the tryptic fragments contained more than one modification, i.e. a Cys degradation product in close proximity to a dehydrated amino acid. Several novel cross-links were detected between Cys and Tyr, Cys, Ser and Phe, Cys and Trp, and Trp and Tyr. Photo-induced protein fragmentation was detected specifically at or in close proximity to the disulfide bond between T6 and T16. An in-house packed 75cm nano-column enabled us to resolve various isomers/diastereomers of the photo-degradation products. A comprehensive analysis of photodegradation products revealed a variety of novel photo-products, including cross-links, originating from disulfide degradation. The mechanisms of product formation are discussed.

Understanding the Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 1 (MMDS1)—Impact of a Disease-Causing Gly208Cys Substitution on Structure and Activity of NFU1 in the Fe/S Cluster Biosynthetic Pathway

Iron–sulfur (Fe/S)-cluster-containing proteins constitute one of the largest protein classes, with varied functions that include electron transport, regulation of gene expression, substrate binding and activation, and radical generation. Consequently, the biosynthetic machinery for Fe/S clusters is evolutionarily conserved, and mutations in a variety of putative intermediate Fe/S cluster scaffold proteins can cause disease states, including multiple mitochondrial dysfunctions syndrome (MMDS), sideroblastic anemia, and mitochondrial encephalomyopathy. Herein, we have characterized the impact of defects occurring in the MMDS1 disease state that result from a point mutation (Gly208Cys) near the active site of NFU1, an Fe/S scaffold protein, via an in vitro investigation into the structural and functional consequences. Analysis of protein stability and oligomeric state demonstrates that the mutant increases the propensity to dimerize and perturbs the secondary structure composition. These changes appear to underlie the severely decreased ability of mutant NFU1 to accept an Fe/S cluster from physiologically relevant sources. Therefore, the point mutation on NFU1 impairs downstream cluster trafficking and results in the disease phenotype, because there does not appear to be an alternative in vivo reconstitution path, most likely due to greater protein oligomerization from a minor structural change.

Critical Role of a Novel Biological Marker GALNT14 Expression in Different Cancer Types

O type-glycosylation which binding of monosaccharides to Ser and Thr residues on receptor proteins is one of the most common posttranslational modifications. It regulates a variety of biological processes that including cell growth, signaling, protein stability and traffic analysis and cell adhesion [1]. O-type glycosylation is present in humans with at least 20 members, from GALNTl to 14 and from GALNTI to L6. It is catalyzed by GalNAc transferases which a large polypeptide in the Golgi complex [2]. In addition to their role in normal cellular processes, changes in O-glycan compositions alter GALNT expression and cause cancer.

Improved insights into protein thermal stability: from the molecular to the structurome scale

Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability-at the structurome level-contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Pairwise contact energy statistical potentials can help to find probability of point mutations.

To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β)8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than iMutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc.

Large scale analysis of protein stability in OMIM disease related human protein variants.

BackgroundModern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability.ResultsWe develop INPS3D, a new predictor based on protein structure for computing the effect of single residue variations on protein stability (ΔΔG), scoring at the state-of-the-art (Pearson’s correlation value of the regression is equal to 0.72 with mean standard error of 1.15 kcal/mol on a blind test set comprising 351 variations in 60 proteins). We then filter 368 OMIM disease related proteins known with atomic resolution (where the three dimensional structure covers at least 70 % of the sequence) with 4717 disease related single residue variations and 685 polymorphisms without clinical consequence. We find that the effect on protein stability of disease related variations is larger than the effect of polymorphisms: in particular, by setting to |1 kcal/mol| the threshold between perturbing and not perturbing variations of the protein stability, about 44 % of disease related variations and 20 % of polymorphisms are predicted with |ΔΔG| > 1 kcal/mol, respectively. A consistent fraction of OMIM disease related variations is however predicted to promote |ΔΔG| ≤ 1 kcal/mol and we focus here on detecting features that can be associated to the thermodynamic property of the protein variant. Our analysis reveals that some 47 % of disease related variations promoting |ΔΔG| ≤ 1 are located in solvent exposed sites of the protein structure. We also find that the increase of the fraction of variations that in proteins are predicted with |ΔΔG| ≤ 1 kcal/mol, partially relates with the increasing number of the protein interacting partners, corroborating the notion that disease related, non-perturbing variations are likely to impair protein-protein interaction (70 % of the disease causing variations, with high accessible surface are indeed predicted in interacting sites). The set of OMIM surface accessible variations with |ΔΔG| ≤ 1 kcal/mol and located in interaction sites are 23 % of the total in 161 proteins. Among these, 43 proteins with some 327 disease causing variations are involved in signalling, structural biological processes, development and differentiation.ConclusionsWe compute the effect of disease causing variations on protein stability with INPS3D, a new state-of-the-art tool for predicting the change in ΔΔG value associated to single residue substitution in protein structures. The analysis indicates that OMIM disease related variations in proteins promote a much larger effect on protein stability than polymorphisms non-associated to diseases. Disease related variations with a slight effect on protein stability (|ΔΔG| < 1 kcal/mol) frequently occur at the protein accessible surface suggesting that they are located in protein-protein interactions patches in putative human biological functional networks. The hypothesis is corroborated by proving that proteins with many disease related variations that slightly perturb protein stability are on average more connected in the human physical interactome (IntAct) than proteins with variations predicted with |ΔΔG| > 1 kcal/mol.

Three easy pieces

BackgroundDifferential scanning calorimetry is a powerful method that provides a complete thermodynamic characterization of the stability of a protein as a function of temperature. There are, however, circumstances that preclude a complete analysis of DSC data. The most common ones are irreversible denaturation transitions or transitions that take place at temperatures that are beyond the temperature limit of the instrument. Even for a protein that undergoes reversible thermal denaturation, the extrapolation of the thermodynamic data to lower temperatures, usually 25°C, may become unreliable due to difficulties in the determination of ΔCp. MethodsThe combination of differential scanning calorimetry and isothermal chemical denaturation allows reliable thermodynamic analysis of protein stability under less than ideal conditions. Results and conclusionsThis paper demonstrates how DSC can be used in combination with chemical denaturation to address three different scenarios: 1) estimation of an accurate ΔCp value for a reversible denaturation using as a test system the envelope HIV-1 glycoprotein gp120; 2) determination of the Gibbs energy of stability in the region in which thermal denaturation is irreversible using HEW lysozyme at different pH values; and, 3) determination of Gibbs energy of stability for a thermostable protein, thermolysin. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Robust and convenient analysis of protein thermal and chemical stability.

We present the software CDpal that is used to analyze thermal and chemical denaturation data to obtain information on protein stability. The software uses standard assumptions and equations applied to two-state and various types of three-state denaturation models in order to determine thermodynamic parameters. It can analyze denaturation monitored by both circular dichroism and fluorescence spectroscopy and is extremely flexible in terms of input format. Furthermore, it is intuitive and easy to use because of the graphical user interface and extensive documentation. As illustrated by the examples herein, CDpal should be a valuable tool for analysis of protein stability.