Ramachandran plot on the web (2.0)

The Ramachandran plot displays the main chain conformation angles (Phi and Psi) of the polypeptide chain of a protein molecule. The paper reports the updated version of the Ramachandran plot web server and has several improved options for displaying the conformation angles in various regions. In addition, options are provided to display the conformation angles in various secondary structural elements and regions within the user specified Phi and Psi values in the plot. The updated version is accessible at the following URL: http://dicsoft1.physics.iisc.ernet.in/rp/.     

CADB: Conformation Angles DataBase of proteins

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/.     

SSEP: Secondary structural elements of proteins

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the alpha-helical segments and beta-strand fragments of varying lengths. In addition, it also contains the information about 3(10)-helix, beta- and nu-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/.     

TALI: local alignment of protein structures using backbone torsion angles

Torsion angle alignment (TALI) is a novel approach to local structural motif alignment, based on backbone torsion angles (phi, psi) rather than the more traditional atomic distance matrices. Representation of a protein structure in the form of a sequence of torsion angles enables easy integration of sequence and structural information, and adopts mature techniques in sequence alignment to improve performance and alignment quality. We show that TALI is able to match local structural motifs as well as identify global structural similarity. TALI is also compared to other structure alignment methods such as DALI, CE, and SSM, as well as sequence alignment based on PSI-BLAST; TALI is shown to be equally successful as, or more successful than, these other methods when applied to challenging structural alignments. The inference of the evolutionary tree of class II aminoacyl-tRNA synthetase shows the potential for TALI in estimating protein structural evolution and in identifying structural divergence among homologous structures. Availability: http://redcat.cse.sc.edu/index.php/Project:TALI/.     

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a–p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and β-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.     

STRALCP--structure alignment-based clustering of proteins

Protein structural annotation and classification is an important and challenging problem in bioinformatics. Research towards analysis of sequence-structure correspondences is critical for better understanding of a protein's structure, function, and its interaction with other molecules. Clustering of protein domains based on their structural similarities provides valuable information for protein classification schemes. In this article, we attempt to determine whether structure information alone is sufficient to adequately classify protein structures. We present an algorithm that identifies regions of structural similarity within a given set of protein structures, and uses those regions for clustering. In our approach, called STRALCP (STRucture ALignment-based Clustering of Proteins), we generate detailed information about global and local similarities between pairs of protein structures, identify fragments (spans) that are structurally conserved among proteins, and use these spans to group the structures accordingly. We also provide a web server at http://as2ts.llnl.gov/AS2TS/STRALCP/ for selecting protein structures, calculating structurally conserved regions and performing automated clustering.     

Multiple flexible structure alignment using partial order graphs

MOTIVATION: Existing comparisons of protein structures are not able to describe structural divergence and flexibility in the structures being compared because they focus on identifying a common invariant core and ignore parts of the structures outside this core. Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins. RESULTS: A new method of multiple protein structure alignment, POSA (Partial Order Structure Alignment), was developed using a partial order graph representation of multiple alignments. POSA has two unique features: (1) identifies and classifies regions that are conserved only in a subset of input structures and (2) allows internal rearrangements in protein structures. POSA outperforms other programs in the cases where structural flexibilities exist and provides new insights by visualizing the mosaic nature of multiple structural alignments. POSA is an ideal tool for studying the variation of protein structures within diverse structural families. AVAILABILITY: POSA is freely available for academic users on a Web server at http://fatcat.burnham.org/POSA     

Interdomain contact regions and angles between adjacent short consensus repeat domains

The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers that consist of two to 12 amino acid residues. Based on experimentally determined structures the neighbouring SCR domains interact with each other at the so-called hinge or interdomain contact region. The functions mediated by the SCR domains have been studied using mutagenesis but the possible effects of the mutations on the hinge regions and interdomain angles have not been analysed. In this study, the linker and three loops in conserved locations were found to be responsible for the interdomain contact regions of all the solved experimental structures. The interdomain contact regions were identified in sequences of 140 human SCR domain pairs, and distinct hydrophobic and charge features were found in different subsets of SCR proteins and functional domains. To compare the possible associations of the interdomain contact region characteristics to the interdomain orientations all the experimentally solved SCR structures were subjected to a uniform calculation of tilt, twist, and skew angles that define the interdomain orientation. The twist and skew angles were found to have a linear correlation and the spatial location of one loop of the N-terminal domain (N#1) was found to have an effect on the skew angle. Thus, we describe location of the interdomain contact regions in primary structures of SCR domains and report that the orientation of adjacent SCR domains is not random and depends partially on the interdomain contact regions. On the basis of these results, mutations within the interdomain contact regions and subsequent loss-of-function effects caused by changes in the interdomain orientation can be avoided in mutagenesis studies.     

AlphaCutter: Efficient removal of non-globular regions from predicted protein structures

A huge number of high-quality predicted protein structures are now publicly available. However, many of these structures contain non-globular regions, which diminish the performance of downstream structural bioinformatic applications. In this study, we develop AlphaCutter for the removal of non-globular regions from predicted protein structures. A large-scale cleaning of 542,380 predicted SwissProt structures highlights that AlphaCutter is able to (1) remove non-globular regions that are undetectable using pLDDT scores and (2) preserve high integrity of the cleaned domain regions. As useful applications, AlphaCutter improved the folding energy scores and sequence recovery rates in the re-design of domain regions. On average, AlphaCutter takes less than 3 s to clean a protein structure, enabling efficient cleaning of the exploding number of predicted protein structures. AlphaCutter is available at https://github.com/johnnytam100/AlphaCutter . AlphaCutter-cleaned SwissProt structures are available for download at https://doi.org/10.5281/zenodo.7944483 .     

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of protein domains in various families. The latest updated version (Release 2.1) comprises of 844 families of homologous proteins involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned with every other member in the same family using two proteins at a time. In addition, an alignment of multiple structures has also been performed using all the members in a family. Every family with at least three members is associated with two dendrograms, one based on a structural dissimilarity metric and the other based on similarity of topologically equivalenced residues for every pairwise alignment. Apart from these multi-member families, there are 817 single member families in the updated version of PALI. A new feature in the current release of PALI is the integration, with 3-D structural families, of sequences of homologues from the sequence databases. Alignments between homologous proteins of known 3-D structure and those without an experimentally derived structure are also provided for every family in the enhanced version of PALI. The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali.     

A data bank merging related protein structures and sequences.

A data collection which merges protein structural and sequence information is described. Structural superpositions amongst proteins with similar main-chain fold were performed or collected from the literature. Sequences taken from the protein primary structure databases were associated with the multiple structural alignments providing they were at least 50% homologous in residue identity to one of the structural sequences and at least 50% of the structural sequence residues were alignable. Such restrictions allow reasonable confidence that the primary sequences share the conformation of the tertiary structural templates, except in the less conserved loop regions. Multiple structural superpositions were collected for 38 familial groups containing a total of 209 tertiary structures; 45 structures had no superposable mates and were used individually. Other information is also provided as main-chain and side-chain conformational angles, secondary structural assignments and the like. Wedding the primary and tertiary structural data resulted in an 8-fold increase of data bank sequence entries over those associated with the known three-dimensional architectures alone.     

Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach

Abstract

Analysis of the conformational space populated by the torsion angles and the correlation between the conformational energy and the sequence of DNA are important for fully understanding DNA structure and function. Presence of seven variable torsion angles about single covalent bonds in DNA main chain puts a big challenge for such analysis. We have carried out restrained energy minimization studies for four representative dinucleosides, namely d(ApA):d(TpT), d(CpG):d(CpG), d(GpC):d(GpC) and d(CpA):d(TpG) to determine the energy hyperspace of DNA in context to the values of the torsion angles and the structural properties of the DNA conformations populating the favorable regions of this energy hyperspace. The torsion angles were manipulated by constraining their values at the reference points and then performing energy minimization. The energy minima obtained on the potential energy contour plots mostly correspond to the conformations populated in crystal structures of DNA. Some novel favorable conformations that are not present in crystal structure data are also found. The plots also suggest few low energy routes for conformational transitions or the associated energy barrier heights. Analyses of base pairing and stacking possibility reveal structural changes accompanying these transitions as well as the flexibility of different base steps towards variations in different torsion angles.     

Statistical measures on residue-level protein structural properties

The atomic-level structural properties of proteins, such as bond lengths, bond angles, and torsion angles, have been well studied and understood based on either chemistry knowledge or statistical analysis. Similar properties on the residue-level, such as the distances between two residues and the angles formed by short sequences of residues, can be equally important for structural analysis and modeling, but these have not been examined and documented on a similar scale. While these properties are difficult to measure experimentally, they can be statistically estimated in meaningful ways based on their distributions in known proteins structures. Residue-level structural properties including various types of residue distances and angles are estimated statistically. A software package is built to provide direct access to the statistical data for the properties including some important correlations not previously investigated. The distributions of residue distances and angles may vary with varying sequences, but in most cases, are concentrated in some high probability ranges, corresponding to their frequent occurrences in either α-helices or β-sheets. Strong correlations among neighboring residue angles, similar to those between neighboring torsion angles at the atomic-level, are revealed based on their statistical measures. Residue-level statistical potentials can be defined using the statistical distributions and correlations of the residue distances and angles. Ramachandran-like plots for strongly correlated residue angles are plotted and analyzed. Their applications to structural evaluation and refinement are demonstrated. With the increase in both number and quality of known protein structures, many structural properties can be derived from sets of protein structures by statistical analysis and data mining, and these can even be used as a supplement to the experimental data for structure determinations. Indeed, the statistical measures on various types of residue distances and angles provide more systematic and quantitative assessments on these properties, which can otherwise be estimated only individually and qualitatively. Their distributions and correlations in known protein structures show their importance for providing insights into how proteins may fold naturally to various residue-level structures.     

CASTp: Computed Atlas of Surface Topography of proteins

Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. CASTp can be used to study surface features and functional regions of proteins. CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu.     

Structures, basins, and energies: a deconstruction of the Protein Coil Library

Globular proteins adopt complex folds, composed of organized assemblies of alpha-helix and beta-sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither alpha-helix nor beta-strand, extracted from high-resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the phi,psi map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least-studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed ,psi distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with alpha-helices, strands of beta-sheet, canonical beta-turns, and polyproline II conformers comprise approximately 90% of all protein structure.     

Mutants of monomeric red fluorescent protein mRFP1 at residue 66: Structure modeling by molecular dynamics and search for correlations with spectral properties

To study the interrelation between the spectral and structural properties of fluorescent proteins, structures of mutants of monomeric red fluorescent protein mRFP1 with all possible point mutations of Glu66 (except replacement by Pro) were simulated by molecular dynamics. A global search for correlations between geometrical structure parameters and some spectral characteristics (absorption maximum wavelength, integral extinction coefficient at the absorption maximum, excitation maximum wavelength, emission maximum wavelength, and quantum yield) was performed for the chromophore and its 6 A environment in mRFP1, Q66A, Q66L, Q66S, Q66C, Q66H, and Q66N. The correlation coefficients (0.81-0.87) were maximal for torsion angles in phenolic and imidazolidine rings as well as for torsion angles in the regions of connection between these rings and chromophore attachment to beta-barrel. The data can be used to predict the spectral properties of fluorescent proteins based on their structures and to reveal promising positions for directed mutagenesis.     

SMS 2.0: an updated database to study the structural plasticity of short peptide fragments in non-redundant proteins

The function of a protein molecule is greatly influenced by its three-dimensional (3D) structure and therefore structure prediction will help identify its biological function. We have updated Sequence, Motif and Structure (SMS), the database of structurally rigid peptide fragments, by combining amino acid sequences and the corre-sponding 3D atomic coordinates of non-redundant (25%) and redundant (90%) protein chains available in the Protein Data Bank (PDB). SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 resi-dues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermedi-ate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the pro-gram structural alignment of multiple proteins (STAMP) and the popular JAVA plug-in (Jmol) is deployed for visualization. In addition, functionalities are provided to search for the occurrences of the sequence motifs in other structural and sequence databases like PDB, Genome Database (GDB), Protein Information Resource (PIR) and Swiss-Prot. The updated database along with the search engine is available over the World Wide Web through the following URL http://cluster.physics.iisc.ernet.in/sms/.     

600 ps Molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase

Molecular dynamics simulations of the catalytic subunit of cAMP dependent protein kinase (cAPK) have been performed in an aqueous environment. The relations among the protein hydrogen‐bonding network, secondary structural elements, and the internal motions of rigid domains were examined. The values of fluctuations of protein dihedral angles during dynamics show quite distinct maxima in the regions of loops and minima in the regions of α‐helices and β‐strands. Analyses of conformation snapshots throughout the run show stable subdomains and indicate that these rigid domains are constrained during the dynamics by a stable network of hydrogen bonds. The most stable subdomain during the dynamics was in the small lobe including part of the carboxy‐terminal tail. The most significant flexible region was the highly conserved glycine‐rich loop between β strands 1 and 2 in the small lobe. Many of the main chain dihedral angle changes measured in a comparison of the crystallographic structures of “open” and “closed” conformations of cAPK correspond to the highly flexible residues found during dynamics. © 1999 John Wiley & Sons, Inc. Biopoly 50: 513–524, 1999     

Relation between the spectral NMR parameters and conformation characteristics of the amino acid residue backbone. Analysis of elements of the secondary structure of proteins

Based on the analysis of the proton-proton distance dependences from the conformational characteristics of the L-amino acid residues, the correlation diagram of the NOE cross peak intensity waited values with the regions of the sterically allowed space (phi, psi) was proposed. The method for determining the dihedral angles phi, psi values using the information about NOE cross peak intensities was elaborated. By the model spectral NMR parameters of the bovine pancreatic trypsin inhibitor, it is shown that the accuracy of the angles phi, psi determination exceed the corresponding accuracy provided by other methods of the structural interpretation of the two-dimensional NMR spectroscopy data. The analysis of the waited spectral NMR parameters for the different types of protein regular secondary structures and beta-turns was performed.     

A proteomic Ramachandran plot (PRplot)

Each protein structure can be characterized by the average values of the main chain torsion angles ? and ψ and, as a consequence, be plotted on a bidimensional diagram, which resembles the Ramachandran plot. Here, we describe a proteomic ?–ψ plot (PRplot) where each protein structure is associated with one point, allowing in this way to represent the entire protein structure universe. It was verified that the PRplot is a robust tool since it does not depend on the dimension of the proteins, on the crystallographic resolution of the structures, nor on the biological source; moreover, it is little affected by disordered and structurally uncharacterized residues. The proteins mapped on the PRplot tend to cluster in three regions that correspond to the structures rich in alpha-helices, in beta-strands, and in both helices and strands, and are distributed along a sigmoidal curve that connect these three highly populated regions. PRplots are a unique instrument to project all protein structures on a single bidimensional plane where the entire structural complexity is reduced to a striking simplicity, with the sigmoid curve clearly delineating the space fraction accessible to a stable protein.