Sulfur metabolism, the oldest known redox processes mediated by dsr operon, maintains the environmental sulfur balance. DsrP protein from the dsr operon transports electrons from the environmental sulfur substrates for per- forming the reactions. We therefore, tried to analyze the probable molecular basis of DsrP proteins using only the se- quence information. We also tried to predict the effects of the mutations present in the sequences of DsrP proteins and a phylogenetic relationship between the organisms possessing the operon has been drawn. Our study may therefore shed light in the hitherto unknown biochemical mechanism of the sulfur oxidation process through dsr operon. In the present work we made an endeavour to character- ize the DsrP protein at the sequence level. We analyzed the amino acid sequences of DsrP proteins from 24 different organisms. We predicted the putative conserved domains present in the protein as well the mapped the amino acids present in the conserved domain. Comparison of the se- quences of DsrP protein from the 24 different organisms revealed the presence of certain mutations. We also predicted the effects of those mutations present in the conserved do- main of DsrP protein and correlated the effects of mutations with the environmental distributions of the microorganisms. Till date there are no previous reports that deal with the analyses of the DsrP proteins at the sequence level. This work is therefore one of its kind. Further extension of the work would involve the identifications of the structural de- tails of the interactions of DsrP proteins with other members of the dsr operon. Since there are no previous reports regard- ing DsrP proteins our work would therefore be important to analyze the biochemical details of the dsr operon.
Conformation search procedure is carried out to generate an ensemble of conformations that could be used for purposes such as to address the problem of ligand and receptor flexibility during molecular docking, protein structure predictions, loop modeling and to calculate binding properties.Two important aspects have been discussed, the criteria of different conformations for the purpose of effective conformation sampling in systematic conformation searches, and the redundancies of using random number generators in random searches.
Texas Red dyes were used to partially label proteins for crystallization in both detergent and lipidic mesophases.Fluorescence detection of Texas Red can then be used to differentiate the protein crystals from salt crystals and other phase separations in the crystallization drop.Whereas ultraviolet light absorption and fluorescence of protein crystals in lipidic meso phase crystallization trials using glass sandwich plates was difficult to discern, the fluorescence of the partially labeled protein can be used to distinguish protein crystals.With as little as 0.05% Texas Red labeling of the protein, protein crystals showed up very clearly in both detergent and the lipid meso-phase crystallization setups.
A computational analysis on the CH/ interactions in a group of 49 therapeutic proteins was investigated. A total of 77 CH/ interactions were observed. The donor atom contribution to CH/ interactions was mainly from aromatic residues. Long-range CH/ interactions are the predominant type of interactions in therapeutic proteins data set. The secondary structure preference, solvent accessibility and stabilization centers of these of CH/ interacting residues were estimated. 73% of the donor residues and 65% of the acceptor residues were highly conserved.
We describe a novel method for predicting G-protein coupled receptor (GPCR) - G-protein coupling selectivity using amino acid properties of specific residues in GPCR sequences. We have evaluated various amino acid properties obtained with experimental or theoretical studies. The GPCRs having reliable G-protein binding information were collected from Guide to Receptors and Channels (GRAC) and gpDB databases, and these sequences were aligned with the amino acid sequence of bovine rhodopsin, whose structure is known, to identify positions of each amino acid residue and its secondary structure. The collected properties were used as feature values to calculate Fisher's ratio (FR) for each residue in GPCRs related with rhodopsin residue numbers. Some amino acid properties with high FR value were picked up as the effective characteristics for selecting G-protein type, and they were used as feature vectors in support vector machine (SVM) to predict GPCR - G-protein coupling selectivity. Applying this method to known GPCR sequences, each binding G-protein is predicted with high sensitivity and specificity of more than 96%. This result strongly suggests that the amino acid properties of specific residues are appreciably important for GPCR - G-protein coupling to determine G- protein binding selectivity and our method could be an effective tool to investigate the mechanism of GPCR - G-protein coupling through site directed mutagenesis experiments.
Proteins are grouped into various families according to their evolutionary origin. Analyzing such types of families based on their inter residue interactions is crucial because algorithms that search for pair wise homologies can miss important relations and produce false hits. Several statistical models have been created to aid in the classification but so far had only partial success. In this work, we have analyzed the variation of long-range contacts in different bin intervals as well as characterized the long-range order in a set of 37 families of homologous proteins belonging to different structural classes. The results reveal the specific long-range contacts as well as variation of long-range order in different structural classes. The pair-wise residue preference to form long-range contacts reveals the dominance of hydrophobic residues irrespective of the structural class. We also provide visual examples of long-range contact network pattern in the different structural classes. BACKGROUND Proteins evolved from a common ancestor are said to be homologues and to constitute a family with potentially similar structures, functions, and interactions. Analysis of a set of similarly folded proteins with distinct amino acid seq- uences, such as homologues, can help in identifying residues and regions of polypeptide chains that are likely to be important in the formation and stability of the fold. The problem of identifying real protein families based on amino acid sequence conservation has been the subject of extensive debate, because algorithms that search for pair wise homologies can miss important relations and produce false hits. Automatic classification of proteins into homo- logous super families, by looking at their three dimensional structure has been a long goal for scientists studying proteins. Several statistical models have been created to aid in the classification but so far had only partial success. Correct functional and evolutionary classification of new structures is difficult for distantly related proteins and error- prone using simple statistical scores based on sequence or structure similarity. There are databases, which contains homologous families of proteins that have been classified by their structural classes and folds. A fully automated database of protein sequences patterns derived from the analysis of the conser- ved residues that are predicted to be functional in struc- turally-aligned homologous families is the HOMSTRAD database (1) and PALI (2) is a database that consists of 1922 protein families containing over 13,500 protein domains. The SCOP (Structural Classification of Proteins) (3) data-
Proteins are one of the most versatile biomolecules and they perform diverse functions in living organisms.The function of a protein is mainly dictated by its structure and understanding the structure-function relationship of proteins is a challenging task.The structural biology of proteins aids to understand the structure-function relationship, such as the three-dimensional structure determination of proteins and their complexes, structural analysis of proteins, molecular dynamics simulations, protein folding rates, protein stability and protein interactions.This special issue on "Structural biology of proteins" addresses most of these aspects with latest developments.Kumarevel revealed the anti-termination mechanism of proteins through structural and functional analysis of a protein-RNA complex, HutP.Sudandiradoss and Sethumadhavan performed molecular docking simulations of scorpin toxins and human voltage-gated potassium channel and identified the key residues for binding.The influence of disulfide bonds in antifungal proteins and peptides has been reported with molecular dynamics simulations by Jayanthi et al.Saravanan and Selvaraj analyzed the long-range contacts and networks in homologous family of proteins.Gromiha showed the intrinsic relationship of amino acid composition/occurrence with topological parameters and folding rates.The relative contributions of strong and weak interactions in epidermal growth factor receptor tyrosine kinase have been evaluated by Swarnadeepa et al.Huang et al. developed a fuzzy query method with human readable rules for predicting the stability of proteins upon amino acid replacements.Further, a novel method has been proposed for predicting the GPCR-G protein coupling selectivity using amino acid properties by Yabuki et al.In essence, this special issue comprehends the exciting developments in the area of structural biology of proteins and it will be a valuable resource for computational biologists, biochemists, biophysicists, bioinformaticians and researchers working in the field of proteins.Finally, I would like to thank all the authors for their contributions and cooperation to complete the task.
In this work, we study simples phosphazenes models, such as R-[R 2 P=N] n -X, with (X = H, F, OH), (R= H, F) and (n = 1, 2 and 3) with an attempt to answer the type of Natural Hybrid Orbital (NHO) able to form this -bond in the phosphazene-Na + complex and the Na + effect on the geometry and the electronic distribution of the studied molecules by using the HF and DFT studies of electronics, molecular structures and Natural Bond Orbital (NBO) analysis.The substituent effect of the fluorine atom acceptor and the OH group donor is studied.The phosphazene polymers doped by Na + cation, linearize all the PNP bond angles.
We report structural model of the human voltage-gated potassium ion channel Kv1.3 obtained based on the crystallographic structure of KcsA by homology modeling.Molecular docking simulations were performed between the model structure of Kv1.3 channel with three short-chain four disulphide bridged scorpion toxins HsTX1 from the venom of Heterometrus spinnifer (Scorpionidae), maurotoxin (MTX) from Scorpiomaurus palmatus and Pandinus toxin 1(Pi1) from Pandinus imperator which belongs to the -KTx6 subfamily.By integrating the homology modeling and docking simulations we obtained the three dimensional structures of toxin-channel complexes.The final docked complexes were then subject to minimization with CHARMM force field and investigated key interacting residues, electrostatic interaction energies, binding free energies, disulphide bridge pairing determination, folding pattern, hydrogen bond formation, hydrophobic contacts and flexibilities between selected scorpion toxins to the Kv1.3 channel.
The solution structure of a novel plant defensin (PhD1) contains a fifth disulfide bond, unlike other plant defensins, which have four disulfide bonds. The present study aims to better understand the stability, thermal dependence and the role of disulfide bonds in the tertiary structure of PhD1 using Molecular Dynamics (MD) simulations. The secondary structures are intact in the native structure simulated at 300 K. However, in the mutant structures a small variation is observed. A significant shift in the peptide conformation is observed when the additional fifth disulfide bond (Cys7-Cys23) is mutated. No large change in the tertiary structure conformation is observed till 400 K, which demonstrates the high thermal stability of the protein. Here, we also show that the mutation of disulfide bonds did not result in a drastic conformational change. The antifungal property along with high structural stability of the plant defensin protein makes it a promising candidate for the development of novel fungicides.
Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms. In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms. Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA. This review de- scribes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the acti- vated conformation of HutP, initiated by the coordination of L-histidine and Mg 2+ ions, based on our previous and re- cently solved crystal structures (uncomplexed HutP, HutP-Mg 2+ , HutP-L-histidine, HutP-Mg 2+ -L-histidine, HutP-Mg 2+ -L- histidine-RNA (21-mer and 55-mer)). In this anti-termination process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem. By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termina- tion of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degrada- tion.
Structures of porphyrin-containing proteins from the Protein Data Bank (PDB) Select January 2007, were searched in order to find and systematically characterize hydrogen bonds and hydrophobic interactions of porphyrins in proteins.The results revealed that every porphyrin is involved in at least one hydrogen bond, most of the porphyrins form several, while some of them form up to thirteen hydrogen bonds.In most of the hydrogen bonds propionate groups of porphyrins interact with side-chains of residues.The most frequently observed donor is side chain of arginine.Histidine, lysine, threonine, serine and tyrozine form substantial number of hydrogen bonds too.The study has revealed that hydrophobic interactions are common between porphyrin and protein.Side-chains hydrophobic interactions are more frequent than those with backbone.The average conservation score for the amino acids making hydrogen bonds (7.2) and hydrophobic interactions (7.3) is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions (5.7) with the porphyrin, indicating importance of hydrogen bonds and hydrophobic interactions with the porphyrin.
Understanding the relationship between amino acid sequences and folding rates of proteins is an important task in computational and molecular biology.It has been shown that topological parameters, contact order, long-range order and total contact distance relate well with protein folding rates.In this work, we have systematically analyzed the relationship between amino acid composition/occurrence and protein folding rates along with topological parameters derived from protein three-dimensional structures.We found that the classification of proteins based on their structural classes and folding types (two and three-state proteins) could explain the relationship very well.The amino acid composition showed good correlation with protein folding rates for two-state proteins whereas the correlation is high with amino acid occurrence for three-state proteins.The composition of polar amino acids, Asn, Gln and Ser directly correlated with protein folding rates and a reverse trend was observed between the occurrence of hydrophobic amino acids, Ile and Gly and protein folding rates.The amino acid occurrence showed a positive correlation with folding rates in two-state proteins and a negative correlation in three-state proteins, which reveals that the presence of more number of amino acids in three-state proteins slows down the folding process.The analysis on slow and fast folding proteins showed that the slow folding proteins have appreciable number of residues that form multiple contacts with other residues.Further, we have combined different amino acids based on their chemical properties and analyzed the relationship with protein folding rates, and set up multiple regression equations for predicting protein folding rates.
Temperature-induced unfolding of Klenow-like DNA Pol I ITB-1 was investigated by molecular dynamic simulation, focusing on the key factors that stabilizing the protein.The result showed that the protein unfolded initially by disruptions of the interface between of 5' 3'polymerase and 3' 5' exonuclease domains.Several amino acid residues, Lys374-Glu489 and Lys381-Glu487, form salt bridges at the interface domain and played an important role in the contact between the two domains.These interactions were examined through in silico mutation by comparing the free-energy solvation changes between the wild type and the mutants.The disruption of salt bridges by replacing Glu to Gln at position 487 and 489 caused positive value of G solv , suggesting that the proteins were more unstable.While the substitution of Glu to Asp at position 487 and 489 preserved the electrostatic interaction.The last two mutants showed negative value of G solv , suggesting that the proteins were more stable.All the data suggested that the salt bridges between Lys374-Glu489 and Lys381-Glu487 have an essential role in maintaining the stability of the interface domain of DNA Pol I ITB-1, and thus, the whole structure of the protein.
Epidermal growth factor receptor (EGFR) is a cell membrane receptor serving as a molecular target for Non Small Cell Lung cancer (NSCLC).The aim of the study was to analyze the weak ion interactions taking place in the tyrosine kinase domain of Human and Drosophila EGFR.This study throws light on the environment preferability, stabilizing residues taking part in weak and strong interactions of EGFR TK domain.Analysis of short, medium and long range contacts showed that the cation-interactions are mainly formed by long-range contacts, whereas CH…OC interactions are formed by both long and short range interactions.Except Pro, other non-polar hydrophobic amino acids in Drosophila EGFR TK domain were present in buried environment.However, in humans other than Pro and Ala, which were involved in SS [CH…OC] and SM [NH…OC] interactions, other non-polar hydrophobic amino acid preferred to be in buried environment.The results observed in this study will be useful for understanding the contribution of weak and strong interactions to the stability of EGFR TK domain.Further, the weak interactions have distinct roles in the stability of EGFR TK domain in addition to other conventional strong interactions.The results can lead to the identification of novel targets for NSCLC drugs which in turn will serve as a major break through in the treatment of NSCLC.
The human Protein Kinase R (PKR) is one of the important and critical components of the innate immune response against viral infection.It regulates distinct cellular functions and controls the fate of an RNA molecule in the cell.PKR dephosphorylation is characterised by inhibitory interactions between the kinase domain and the RNA binding domains (RBDs), but the complete structural details and dynamics of the latent state and its activation are not yet clear.Several studies on the activation of double stranded RNA binding domain (dsRBD) of Protein Kinase R (dsRBD-PKR) have been attempted during the last few decades.In order to further investigate on its activation mechanism, we have analysed the backbone [ 1 H-15 N]-dynamics and chemical shift perturbation studies of dsRBD-PKR in the presence of bacteriophage Pf1.Pf1 is known to orient the protein in the presence of external magnetic field and, can be further used to get useful information about the protein properties such as the different dynamic behaviour in multidomain proteins like dsRBD-PKR.These NMR based results improve our basic understanding of the domain flexibilities of dsRBD-PKR where some secondary structural regions of dsRBM1 (dsRNA binding motif 1) show a different behaviour than the one from dsRBM2 (dsRNA binding motif 2) these observations further lead to a better understanding of PKR mechanism where dsRBM1 has more affinity towards RNA as compared to dsRBM2.
Predicting protein mutant stability changes is important for protein design.Many methods have tried to improve prediction accuracy by various models.However, it will be difficult to employ them when the required input information is incomplete.This paper presents a fuzzy query method (named FQ-STAB), which cooperates with a humanreadable rule base to predict stability changes upon single mutations.Firstly, we have effectively established a set of classification rules as a knowledge representation from the thermodynamic database.Next, we applied the proposed method on the rules to predict stability changes under the condition without sufficient information.Further, FQ-STAB has been tested on a data set of single point mutants.The results show that it can be applied to the prediction of stability changes using partial input information, and can also provide the explanation capabilities for the predicted outcome.We have developed a web server for predicting protein stability changes upon single mutations by using fuzzy query mechanism and it is available at http: //bioinformatics.myweb.hinet.net/fqstab.htm.
The three-dimensional structure of a cysteine rich antifungal protein EAFP2 is found to be compact and ex- tremely stable. The rigid nature of the protein is attributed to the presence of five disulfide bonds. However, the effect of individual disulfide bonds on the conformation has not been characterized. Thus, Molecular Dynamics (MD) simulations are used to explicate the influence of disulfide bonds on the conformation. In the present study, the cysteine residues in the native structure are mutated to alanine and the structural characteristics and conformational dynamics of the native and mutant structures are analyzed to better understand the effect of disulfide bonds on the tertiary structure. The simulated native and single mutant structures are found to posses similar conformations, indicating that loss of disulfide bond did not affect the tertiary structure conformation greatly. However, in the single mutant (C7A) structure, the N and C-terminal segments are found to be different. It is also interesting to note that the loss of disulfide bond between Cys35 and Cys39 actually resulted in a more compact structure.
Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms.In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms.Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA.This review describes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the activated conformation of HutP, initiated by the coordination of L-histidine and Mg 2+ ions, based on our previous and recently solved crystal structures (uncomplexed HutP, HutP-Mg 2+ , HutP-L-histidine, HutP-Mg 2+ -L-histidine, HutP-Mg 2+ -Lhistidine-RNA (21-mer and 55-mer)).In this anti-termination process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem.By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termination of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degradation.
