SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-Redundant Proteins

Abstract

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 corresponding 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 residues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermediate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the program 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/.

Search and Analysis of Identical Reverse Octapeptides in Unrelated Proteins

“…In recent years, several methods based on similarity and dissimilarity comparison have advanced rapidly to understand the structure, function and property of proteins [25–28] paving the way to the design of novel proteins. For example, Alexander et al [29] designed two proteins with identical sequence apart from one residue mismatch and found that these two proteins adopt completely different folds and functions.…”

Computational Approaches for Structure-Based Functional Annotation of an Uncharacterized Conserved Protein of Acinetobacter baumannii

“…The ProtParam tool of ExPASy [7] was used to record the physicochemical characterization of proteins, including the amino acid sequence composition, instability index, aliphatic index, and GRAVY. Using SMS (v.2.0) [8], the theoretical isoelectric point (pI) and GRAVITY of the SSI32830.1 protein were also determined.…”

“…The domain that appears in identical protein sequences is identified by the NCBI CDD tool. When comparing a test sequence to position-specific rating datasets derived from conserved domain (CD) alignments in the CD protein cluster, CD-Search utilizes RPS-BLAST (8,29). The CD search engine discovered a conserved domain in the protein SSI32830.1 (30-32).…”

“…Ramachandran plot analysis and interactive workplace analysis of the Swiss-Model server were used to compare the modeled tertiary structures to assess the structures' quality [8]. The best template was chosen as a CENP-V/GFA domain-containing protein, and ultimately the tertiary modeled protein structure (Figure 2) was stored in PDB format.…”

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

“…In the past few decades, as a result of advances in datacollection technology and various ambitious structural genomics initiatives, numerous macromolecular crystal structures have been X-ray analysed and deposited in the Protein Data Bank (PDB) (Berman et al, 2000;Balamurugan et al, 2007). The sequence and three-dimensional structure of a protein molecule contains crucial information defining its structure and function (Samaya Mohan et al, 2005;Balamurugan et al, 2005Balamurugan et al, , 2006Gopalakrishnan et al, 2007;Ravella et al, 2012). The primary sequence of a protein is determined by various known sequencing techniques and the three-dimensional structure is resolved by biophysical techniques such as X-ray crystallography, NMR etc.…”