CKAAPs DB: a Conserved Key Amino Acid Positions DataBase

Insights into structure and function of 30S Ribosomal Protein S2 (30S2) in Chlamydophila pneumoniae: A potent target of pneumonia

The gene 30S ribosomal protein S2 (30S2) is identified as a potential drug and vaccine target for Pneumonia. Its structural characterization is an important to understand the mechanism of action for identifying its receptor and/or other binding partners. The comparative genomics and proteomics studies are useful for structural characterization of 30S2 in C. Pneumoniae using different bioinformatics tools and web servers. In this study, the protein 30S2 structure was modelled and validated by Ramachandran plot. It is found that the modelled protein under most favoured "core" region was 88.7% and overall G-factor statistics with average score was -0.20. However, seven sequential motifs have been identified for 30S2 with reference codes (PR0095, PF0038, TIGR01012, PTHR11489, SSF52313 and PTHR11489). In addition, seven structural highly conserved residues have been identified in the large cleft are Lys160, Gly161and Arg162 with volume 1288.83ų and average depth of the cleft was 10.75Å. Moreover, biological functions, biochemical process and structural constituents of ribosome are also explored. The study will be helped us to understand the sequential, structural, functional and evolutionary clues of unknown proteins available in C. Pneumoniae.

Hunting for "key residues" in the modeling of globular protein folding: an artificial neural network-based approach

An approach to modeling globular protein folding based on artificial neural networks (ANNs) is presented. This approach, that can be regarded as an inverse protein folding problem, investigates whether and when a protein fragment needs a specific residue in the center of its primary structure as a necessary condition to fold as observed. To perform this analysis, an ANN has been trained on a set of 55 proteins, searching for a relation between protein fragments modeled by 13alpha torsion angles and the residue corresponding to the central alpha torsion angle of the fragment. The results obtained show that only Asp, Gly, Pro, Ser and Val residues are often a necessary, even though not sufficient, condition to obtain a specific folded fragment structure, playing therefore, the role of "key residue" of this fragment.

iMOTdb--a comprehensive collection of spatially interacting motifs in proteins

Realization of conserved residues that represent a protein family is crucial for clearer understanding of biological function as well as for the better recognition of additional members in sequence databases. Functionally important residues are recognized well due to their high degree of conservation in closely related sequences and are annotated in functional motif databases. Structural motifs are central to the integrity of the fold and require careful analysis for their identification. We report the availability of a database of spatially interacting motifs in single protein structures as well as those among distantly related protein structures that belong to a superfamily. Spatial interactions amongst conserved motifs are automatically measured using sequence similarity scores and distance calculations. Interactions between pairs of conserved motifs are described in the form of pseudoenergies. iMOTdb database provides information for 854,488 motifs corresponding to 60,849 protein structural domains and 22,648 protein structural entries.

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains

We identified key residues from the structural alignment of families of protein domains from SCOP which we represented in the form of sparse protein signatures. A signature-generating algorithm (SigGen) was developed and used to automatically identify key residues based on several structural and sequence-based criteria. The capacity of the signatures to detect related sequences from the SWISSPROT database was assessed by receiver operator characteristic (ROC) analysis and jack-knife testing. Test signatures for families from each of the main SCOP classes are described in relation to the quality of the structural alignments, the SigGen parameters used, and their diagnostic performance. We show that automatically generated signatures are potently diagnostic for their family (ROC50 scores typically >0.8), consistently outperform random signatures, and can identify sequence relationships in the "twilight zone" of protein sequence similarity (<40%). Signatures based on 15%-30% of alignment positions occurred most frequently among the best-performing signatures. When alignment quality is poor, sparser signatures perform better, whereas signatures generated from higher-quality alignments of fewer structures require more positions to be diagnostic. Our validation of signatures from the Globin family shows that when sequences from the structural alignment are removed and new signatures generated, the omitted sequences are still detected. The positions highlighted by the signature often correspond (alignment specificity >0.7) to the key positions in the original (non-jack-knifed) alignment. We discuss potential applications of sparse signatures in sequence annotation and homology modeling.

Common features in structures and sequences of sandwich-like proteins

The goal of this work is to define the structural and sequence features common to sandwich-like proteins (SPs), a group of very different proteins now comprising 69 superfamilies in 38 protein folds. Analysis of the arrangements of strands within main sandwich sheets revealed a rigorously defined constraint on the supersecondary substructure that holds true for 94% of known SP structures. The invariant substructure consists of two interlocked pairs of neighboring beta-strands. It is even more typical for centers of SP than the well-known "Greek key" strands arrangement for their edges. As homology among these proteins is not usually detectable even with the most powerful sequence-comparing algorithms, we employed a structure-based approach to sequence alignment. Within the interlocked strands we found 12 positions with fixed structural roles in SP. A residue at any of these positions possesses similar structural properties with residues in the same position of other SPs. The 12 positions lie at the center of the interface between the beta-sheets and form the common geometrical core of SPs. Of the 12 positions, 8 are occupied by only four hydrophobic residues in 80% of all SPs.

Use of conserved key amino acid positions to morph protein folds

By using three-dimensional (3D) structure alignments and a previously published method to determine Conserved Key Amino Acid Positions (CKAAPs) we propose a theoretical method to design mutations that can be used to morph the protein folds. The original Paracelsus challenge, met by several groups, called for the engineering of a stable but different structure by modifying less than 50% of the amino acid residues. We have used the sequences from the Protein Data Bank (PDB) identifiers 1ROP, and 2CRO, which were previously used in the Paracelsus challenge by those groups, and suggest mutation to CKAAPs to morph the protein fold. The total number of mutations suggested is less than 40% of the starting sequence theoretically improving the challenge results. From secondary structure prediction experiments of the proposed mutant sequence structures, we observe that each of the suggested mutant protein sequences likely folds to a different, non-native potentially stable target structure. These results are an early indicator that analyses using structure alignments leading to CKAAPs of a given structure are of value in protein engineering experiments.

Structural genomics of proteins from conserved biochemical pathways and processes

During the past year, X-ray crystallographers and solution NMR spectroscopists have made significant progress towards the complete structural characterization of conserved biochemical pathways and processes. Some of these advances were made in the context of nascent structural genomics programs, which promise to accelerate structural studies of biologically and medically important proteins. The results of high-throughput protein production, crystallization, structure determination, homology modeling and functional annotation published by two such programs have provided insight into the evolution and function of enzymes in the isoprenoid biosynthesis and ribulose monophosphate pathways.