scholarly journals In Silico Functional Annotation of VP 128 Hypothetical Protein from Vibrio parahaemolyticus

10.4194/afs37 ◽  
2021 ◽  
Vol 1 (2) ◽  
Author(s):  
Moslema Jahan Mou ◽  
Sk Injamamul Islam ◽  
Sarower Mahfuj
Keyword(s):  
Protein Interactions ◽  
In Silico ◽  
Vibrio Parahaemolyticus ◽  
Active Sites ◽  
Three Dimensional ◽  
Hypothetical Protein ◽  
Physicochemical Characteristics ◽  
Dimensional Structure ◽  
Structural Domain ◽  
Protein Protein Interactions

Unknown or hypothetical proteins exist, but they have yet to be identified or correlated to gene sequences. Domains of unknown function are proteins that have been identified experimentally but do not have a known functional or structural domain. Using a variety of computational approaches and tools, this research investigated and characterized the likely functional characteristics of a hypothetical protein from Vibrio parahaemolyticus (Accession no. QOS18375.1). The physicochemical characteristics, subcellular localization, three-dimensional structure, protein-protein interactions, and functional elucidation of the protein are all available from this in silico perspective. Protein-protein interactions are investigated using the STRING software and resulted that VP128 putative protein interacts strongly with the GlpX type protein Fructose-1,6-bisphosphatase. The in-silico investigation documented the protein’s hydrophilic nature with predominantly alpha (α) helices in its secondary structure. Furthermore, the protein, according to the research, features a VP128 domain and is thought to bind ribosomal subunits and the top active sites of the model described also. Therefore, the research findings will facilitate the development of new antibacterial drugs against acute gastroenteritis and other serious diseases by providing a better knowledge of the role of VP128 domain.

scholarly journals Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions

2019 ◽  
Vol 47 (W1) ◽  
pp. W331-W337 ◽  
Author(s):  
Ankit A Roy ◽  
Abhilesh S Dhawanjewar ◽  
Parichit Sharma ◽  
Gulzar Singh ◽  
M S Madhusudhan
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Optimal Number ◽  
Dimensional Structure ◽  
Side Chain ◽  
Interface Residue ◽  
Z Score ◽  
Protein Protein Interactions ◽  
Residue Contacts

Abstract Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein–protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts emanate from the main chain or side chain. We tested the score on 174 native interactions for which 100 decoys each were constructed using ZDOCK. The native structure scored better than any of the decoys in 146 cases and was able to rank within the 95th percentile in 162 cases. This easily outperforms a competing method, CIPS. We also benchmarked our scoring scheme on 15 targets from the CAPRI dataset and found that our method had results comparable to that of CIPS. Further, our method is able to analyse higher order protein complexes without the need to explicitly identify chains as receptors or ligands. The PIZSA server is easy to use and could be used to score any input three-dimensional structure and provide a residue pair-wise break up of the results. Attractively, our server offers a platform for users to upload their own potentials and could serve as an ideal testing ground for this class of scoring schemes.

Three-dimensional structure of a regular bacterial surface layer: The HPI-layer of Deinococcus radiodurans

1983 ◽  
Vol 41 ◽  
pp. 438-439
Author(s):  
W. Baumeister ◽  
M. Hahn ◽  
W.O. Saxton
Keyword(s):  
Outer Membrane ◽  
Protein Interactions ◽  
Deinococcus Radiodurans ◽  
Bacterial Species ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Protein Interactions ◽  
Bacterial Surface ◽  
Freeze Dried

Regularly organized surface (RS) layers are a feature common to many bacterial species; they are clearly more abundant than was anticipated even a few years ago. The RS-layers are believed to fulfil a variety of functions in the interaction between the cell and its environment (see e.g. [1]). The so-called HPI-layer of the radiotolerant bacterium Deinococcus radiodurans is a typical example of such a layer: It is composed of a single polypeptide species (Mr 105 kDa) arranged on a hexagonal lattice to form a network that covers the entire surface of the bacterium; it is associated with the outer membrane via hydrophobic protein-protein interactions.Isolated HPI-layer sheets, released from the outer membrane by detergent treatment, have been studied in the electron microscope making extensive use of the present arsenal of preparation techniques: negative staining, (auro- thio)glucose embedding, freeze-dried/unstained, freeze-dried/metal shadowed etc.Because of the notorious problem of lattice imperfections image processing usually followed the strategy of correlation averaging as outlined in some detail elsewhere.

scholarly journals PPI_SVM: Prediction of protein-protein interactions using machine learning, domain-domain affinities and frequency tables

2011 ◽  
Vol 16 (2) ◽  
Author(s):  
Piyali Chatterjee ◽  
Subhadip Basu ◽  
Mahantapas Kundu ◽  
Mita Nasipuri ◽  
Dariusz Plewczynski
Keyword(s):  
Machine Learning ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Prediction Method ◽  
Protein Sequences ◽  
Dimensional Structure ◽  
Support Vector ◽  
Interacting Proteins ◽  
Protein Protein Interactions ◽  
Protein Functions

AbstractProtein-protein interactions (PPI) control most of the biological processes in a living cell. In order to fully understand protein functions, a knowledge of protein-protein interactions is necessary. Prediction of PPI is challenging, especially when the three-dimensional structure of interacting partners is not known. Recently, a novel prediction method was proposed by exploiting physical interactions of constituent domains. We propose here a novel knowledge-based prediction method, namely PPI_SVM, which predicts interactions between two protein sequences by exploiting their domain information. We trained a two-class support vector machine on the benchmarking set of pairs of interacting proteins extracted from the Database of Interacting Proteins (DIP). The method considers all possible combinations of constituent domains between two protein sequences, unlike most of the existing approaches. Moreover, it deals with both single-domain proteins and multi domain proteins; therefore it can be applied to the whole proteome in high-throughput studies. Our machine learning classifier, following a brainstorming approach, achieves accuracy of 86%, with specificity of 95%, and sensitivity of 75%, which are better results than most previous methods that sacrifice recall values in order to boost the overall precision. Our method has on average better sensitivity combined with good selectivity on the benchmarking dataset. The PPI_SVM source code, train/test datasets and supplementary files are available freely in the public domain at: http://code.google.com/p/cmater-bioinfo/.

scholarly journals Occurrence of ordered and disordered structural elements in postsynaptic proteins supports optimization for interaction diversity

2018 ◽  
Author(s):  
Annamária Kiss-Tóth ◽  
Laszlo Dobson ◽  
Bálint Péterfia ◽  
Annamária F. Ángyán ◽  
Balázs Ligeti ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Three Dimensional ◽  
Vital Role ◽  
Dimensional Structure ◽  
Protein Protein Interactions ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Postsynaptic Protein ◽  
Molecular Events ◽  
Characteristic Features

AbstractThe human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, and this duality is also imprinted in the amino acid sequence. We introduce Diversity of Potential Interactions (DPI), a structure and regulation based descriptor to assess the diversity of interactions. Our approach reveals that the postsynaptic proteome has its own characteristic features and these properties reliably discriminate them from other proteins of the human proteome. Our results suggest that postsynaptic proteins are especially susceptible to forming diverse interactions with each other, which might be key in the reorganization of the PSD in molecular processes related to learning and memory.

scholarly journals Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Md. Amran Gazi ◽  
Sultan Mahmud ◽  
Shah Mohammad Fahim ◽  
Md. Rezaul Islam ◽  
Subhasish Das ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Protein Interactions ◽  
In Silico ◽  
Domain Architecture ◽  
Three Dimensional ◽  
Physicochemical Characterization ◽  
Dimensional Structure ◽  
Hypothetical Proteins ◽  
Roc Curve Analysis ◽  
Full Spectrum

Abstract Campylobacter jejuni (C. jejuni) is considered to be one of the most frequent causes of bacterial gastroenteritis globally, especially in young children. The genome of C. jejuni contains many proteins with unknown functions termed as hypothetical proteins (HPs). These proteins might have essential biological role to show the full spectrum of this bacterium. Hence, our study aimed to determine the functions of HPs, pertaining to the genome of C. jejuni. An in-silico work flow integrating various tools were performed for functional assignment, three-dimensional structure determination, domain architecture predictors, subcellular localization, physicochemical characterization, and protein–protein interactions (PPIs). Sequences of 267 HPs of C. jejuni were analyzed and successfully attributed the function of 49 HPs with higher confidence. Here, we found proteins with enzymatic activity, transporters, binding and regulatory proteins as well as proteins with biotechnological interest. Assessment of the performance of various tools used in this analysis revealed an accuracy of 95% using receiver operating characteristic (ROC) curve analysis. Functional and structural predictions and the results from ROC analyses provided the validity of in-silico tools used in the present study. The approach used for this analysis leads us to assign the function of unknown proteins and relate them with the functions that have already been described in previous literature.

The variation of intermolecular contacts in helical aggregates of glutamine synthetase

1978 ◽  
Vol 36 (2) ◽  
pp. 174-175
Author(s):  
T.G. Frey ◽  
D.S. Eisenberg ◽  
P.R. Smith
Keyword(s):  
Glutamine Synthetase ◽  
Protein Interactions ◽  
Divalent Cations ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Protein Interactions ◽  
X Ray Diffraction ◽  
E Coli ◽  
Intermolecular Contacts ◽  
Polypeptide Chains

Glutamine synthetase from E. coli is a large (MW 600,000) oligomeric enzyme composed of twelve identical polypeptide chains of MW 50,000. These twelve subunits are arranged at the vertices of two eclipsed hexagons to produce a structure with symmetry 622 or D6 as shown by electron microscopy and X-ray diffraction. The dodecameric molecule has a hexagonal profile of approximately 140 Å diameter and a thickness of approximately 90 Å. When treated with divalent cations such as Co++, Zn++, Ni++ or Cu++, glutamine synthetase molecules aggregate along their six-fold axes to form long strands and these strands will often wrap around one another to form cables (Fig. 1). The aggregation is completely reversed by the addition of excess Mn++ resulting in regeneration of full enzymatic activjjy. The most regular helical aggregates are formed in the presence of 10 mM Co++ at pH 7.0, and we have used these helical cables to study the three dimensional structure and symmetry of the glutamine synthetase molecule and the types of protein-protein interactions involved in the formation of glutamine synthetase cables.

scholarly journals Crystal structure of PfRh5, an essential P. falciparum ligand for invasion of human erythrocytes

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Lin Chen ◽  
Yibin Xu ◽  
Julie Healer ◽  
Jenny K Thompson ◽  
Brian J Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Severe Form ◽  
Dimensional Structure ◽  
Protein Protein Interactions ◽  
Parasite Invasion ◽  
Obligate Intracellular ◽  
Multiple Protein ◽  
Parasite Survival

Plasmodium falciparum causes the most severe form of malaria in humans and is responsible for over 700,000 deaths annually. It is an obligate intracellular parasite and invades erythrocytes where it grows in a relatively protected niche. Invasion of erythrocytes is essential for parasite survival and this involves interplay of multiple protein–protein interactions. One of the most important interactions is binding of parasite invasion ligand families EBLs and PfRhs to host receptors on the surface of erythrocytes. PfRh5 is the only essential invasion ligand within the PfRh family and is an important vaccine candidate. PfRh5 binds the host receptor basigin. In this study, we have determined the crystal structure of PfRh5 using diffraction data to 2.18 Å resolution. PfRh5 exhibits a novel fold, comprising nine mostly anti-parallel α-helices encasing an N-terminal β-hairpin, with the overall shape being an elliptical disk. This is the first three-dimensional structure determined for the PfRh family of proteins.

scholarly journals Sequence co-evolution gives 3D contacts and structures of protein complexes

2014 ◽  
Author(s):  
Thomas A. Hopf ◽  
Charlotta P.I. Schärfe ◽  
João P.G.L.M. Rodrigues ◽  
Anna G. Green ◽  
Chris Sander ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Evolutionary Sequence ◽  
Protein Protein Interactions ◽  
Interacting Protein ◽  
Protein Protein Interaction ◽  
Unknown Structure

Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequence databases, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution.

scholarly journals β‒hairpin polypeptides by design and selection

2003 ◽  
Vol 17 (2-3) ◽  
pp. 213-230 ◽  
Author(s):  
Nicholas J. Skelton ◽  
Tamas Blandl ◽  
Stephen J. Russell ◽  
Melissa A. Starovasnik ◽  
Andrea G. Cochran
Keyword(s):  
Protein Interactions ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Protein Interactions ◽  
H Nmr ◽  
Helical Peptide ◽  
Conformational Preferences ◽  
Tryptophan Residues ◽  
Hairpin Peptides ◽  
Hairpin Conformation

We have developed polypeptide scaffolds that readily adopt aβ‒hairpin conformation (a pair of antiparallel strands connected by a turn) in solution. The study of such peptides allows us to understand the factors that govern stability and folding of these motifs in proteins, and permits mimicry of functionally important regions of proteins. Spectroscopic and biophysical methods have been used to characterize the conformational preferences and stability of these peptides, with a strong emphasis on using restraints generated from1H NMR spectroscopy to determine their three‒dimensional structure. By optimization of inter‒strand interactions, we have developed highly stable disulfide‒cyclized and linearβ‒hairpin peptides. In particular, tryptophan residues at non‒hydrogen bonded strand sites (NHB) are highly stabilizing. A variety of turn types have been presented from these scaffolds, suggesting that they might generally be useful in turn presentation. Interestingly,β‒hairpin peptides (containing a disulfide and a NHB tryptophan) have recently been discovered as antagonists of protein–protein interactions from naïve peptide libraries displayed on phage. Comparison of one suchβ‒hairpin peptide with anα‒helical peptide of very similar sequence provides further insight into the role that residue type and context play in determining polypeptide conformation.

scholarly journals In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism

2021 ◽  
Vol 19 (4) ◽  
pp. e43
Author(s):  
Lincon Mazumder ◽  
Mehedi Hasan ◽  
Ahmed Abu Rus'd ◽  
Mohammad Ariful Islam
Keyword(s):  
Campylobacter Jejuni ◽  
Protein Interactions ◽  
In Silico ◽  
Functional Annotation ◽  
3D Structure ◽  
Alpha Helix ◽  
Hypothetical Protein ◽  
Random Coil ◽  
Protein Protein Interactions ◽  
In Silico Characterization

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

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