scholarly journals Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach

2012 ◽  
Vol 3 (3) ◽  
pp. 19-31 ◽  
Author(s):  
Vishwesh Venkatraman ◽  
David W. Ritchie
Keyword(s):  
Protein Complexes ◽  
Minimum Weight ◽  
Three Dimensional ◽  
Data Bank ◽  
Search Space ◽  
Ant Colony ◽  
Optimization Approach ◽  
Assembly Problem ◽  
Minimum Weight Spanning Tree ◽  
Component Protein

Many biological processes are governed by large assemblies of protein molecules. However, it is often very difficult to determine the three-dimensional structures of these assemblies using experimental biophysical techniques. Hence there is a need to develop computational approaches to fill this gap. This article presents an ant colony optimization approach to predict the structure of large multi-component protein complexes. Starting from pair-wise docking predictions, a multi-graph consisting of vertices representing the component proteins and edges representing candidate interactions is constructed. This allows the assembly problem to be expressed in terms of searching for a minimum weight spanning tree. However, because the problem remains highly combinatorial, the search space cannot be enumerated exhaustively and therefore heuristic optimisation techniques must be used. The utility of the ant colony based approach is demonstrated by re-assembling known protein complexes from the Protein Data Bank. The algorithm is able to identify near-native solutions for five of the six cases tested. This demonstrates that the ant colony approach provides a useful way to deal with the highly combinatorial multi-component protein assembly problem.

scholarly journals Mutation Sites Are Distant from Remdesivir Binding Site in Human SARS-CoV-2 RNA-Dependent RNA Polymerase

2021 ◽  
Author(s):  
Kunchur Guruprasad
Keyword(s):  
Protein Sequence ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Data Bank ◽  
Rna Dependent Rna Polymerase ◽  
Mutation Site ◽  
Cryo Electron Microscopy ◽  
Reference Protein ◽  
Beta Hairpin ◽  
Geographical Locations

<p>The comparison of 10,929 human SARS-CoV-2 RdRp protein sequences representing six geographical locations with the reference protein sequence in human SARS-CoV-2 genome isolate from Wuhan, China, identified 222 distinct mutation sites in the RdRp protein. The NiRAN and interface domains, Fingers, Palm and Thumb sub-domains were each associated with ~20% or more mutations compared to mutations in N-terminal, beta-hairpin or C-terminal regions of the protein. The Pro4715Leu mutation was predominantly observed in RdRp proteins from all six geographical locations; Africa, Asia, Europe, North America, Oceania and South America. None of the mutation site residues were within 3.2 Å interacting distance from remdesivir as observed in the three-dimensional cryo-electron microscopy structures of RdRp protein complexes available in the Protein Data Bank. Therefore, the mutations in human SARS-CoV-2 RdRp proteins, described in the present work, are not likely to cause resistance to remdesivir binding. Further, the mutations were also not associated with functionally important residues that would affect the enzyme’s function.</p>

scholarly journals Mutation Sites Are Distant from Remdesivir Binding Site in Human SARS-CoV-2 RNA-Dependent RNA Polymerase

2021 ◽  
Author(s):  
Kunchur Guruprasad
Keyword(s):  
Protein Sequence ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Data Bank ◽  
Rna Dependent Rna Polymerase ◽  
Mutation Site ◽  
Cryo Electron Microscopy ◽  
Reference Protein ◽  
Beta Hairpin ◽  
Geographical Locations

<p>The comparison of 10,929 human SARS-CoV-2 RdRp protein sequences representing six geographical locations with the reference protein sequence in human SARS-CoV-2 genome isolate from Wuhan, China, identified 222 distinct mutation sites in the RdRp protein. The NiRAN and interface domains, Fingers, Palm and Thumb sub-domains were each associated with ~20% or more mutations compared to mutations in N-terminal, beta-hairpin or C-terminal regions of the protein. The Pro4715Leu mutation was predominantly observed in RdRp proteins from all six geographical locations; Africa, Asia, Europe, North America, Oceania and South America. None of the mutation site residues were within 3.2 Å interacting distance from remdesivir as observed in the three-dimensional cryo-electron microscopy structures of RdRp protein complexes available in the Protein Data Bank. Therefore, the mutations in human SARS-CoV-2 RdRp proteins, described in the present work, are not likely to cause resistance to remdesivir binding. Further, the mutations were also not associated with functionally important residues that would affect the enzyme’s function.</p>

scholarly journals GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1660
Author(s):  
Serge Pérez ◽  
François Bonnardel ◽  
Frédérique Lisacek ◽  
Anne Imberty ◽  
Sylvie Ricard Blum ◽  
...  
Keyword(s):  
Quaternary Structure ◽  
Graphical Representation ◽  
Dermatan Sulfate ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Keratan Sulfate ◽  
Data Bank ◽  
Scattering Data ◽  
Gag Protein ◽  
X Ray

Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available.

scholarly journals Cobalt-based magnetic Weyl semimetals with high-thermodynamic stabilities

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Wei Luo ◽  
Yuma Nakamura ◽  
Jinseon Park ◽  
Mina Yoon
Keyword(s):  
Tight Binding ◽  
Three Dimensional ◽  
Interlayer Coupling ◽  
First Principles Calculation ◽  
Optimization Approach ◽  
Binding Model ◽  
Nodal Lines ◽  
Weyl Semimetal ◽  
Topological Quantum ◽  
First Time

AbstractRecent experiments identified Co3Sn2S2 as the first magnetic Weyl semimetal (MWSM). Using first-principles calculation with a global optimization approach, we explore the structural stabilities and topological electronic properties of cobalt (Co)-based shandite and alloys, Co3MM’X2 (M/M’ = Ge, Sn, Pb, X = S, Se, Te), and identify stable structures with different Weyl phases. Using a tight-binding model, for the first time, we reveal that the physical origin of the nodal lines of a Co-based shandite structure is the interlayer coupling between Co atoms in different Kagome layers, while the number of Weyl points and their types are mainly governed by the interaction between Co and the metal atoms, Sn, Ge, and Pb. The Co3SnPbS2 alloy exhibits two distinguished topological phases, depending on the relative positions of the Sn and Pb atoms: a three-dimensional quantum anomalous Hall metal, and a MWSM phase with anomalous Hall conductivity (~1290 Ω−1 cm−1) that is larger than that of Co2Sn2S2. Our work reveals the physical mechanism of the origination of Weyl fermions in Co-based shandite structures and proposes topological quantum states with high thermal stability.

scholarly journals A computer-based approach for developing linamarase inhibitory agents

2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Lucas Paul ◽  
Celestin N. Mudogo ◽  
Kelvin M. Mtei ◽  
Revocatus L. Machunda ◽  
Fidele Ntie-Kang
Keyword(s):  
Structure Elucidation ◽  
Three Dimensional ◽  
Data Bank ◽  
Competitive Inhibitor ◽  
Industrial Applications ◽  
Dimensional Structure ◽  
Full Understanding ◽  
The Poor ◽  
Computer Based ◽  
Inhibitory Agents

AbstractCassava is a strategic crop, especially for developing countries. However, the presence of cyanogenic compounds in cassava products limits the proper nutrients utilization. Due to the poor availability of structure discovery and elucidation in the Protein Data Bank is limiting the full understanding of the enzyme, how to inhibit it and applications in different fields. There is a need to solve the three-dimensional structure (3-D) of linamarase from cassava. The structural elucidation will allow the development of a competitive inhibitor and various industrial applications of the enzyme. The goal of this review is to summarize and present the available 3-D modeling structure of linamarase enzyme using different computational strategies. This approach could help in determining the structure of linamarase and later guide the structure elucidation in silico and experimentally.

scholarly journals BanLec-eGFP Chimera as a Tool for Evaluation of Lectin Binding to High-Mannose Glycans on Microorganisms

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 180
Author(s):  
Zorana Lopandić ◽  
Luka Dragačević ◽  
Dragan Popović ◽  
Uros Andjelković ◽  
Rajna Minić ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Lectin Binding ◽  
Three Dimensional ◽  
Data Bank ◽  
Salmonella Typhi ◽  
Excitation Wavelength ◽  
Protein Data Bank Entry ◽  
High Mannose

Fluorescently labeled lectins are useful tools for in vivo and in vitro studies of the structure and function of tissues and various pathogens such as viruses, bacteria, and fungi. For the evaluation of high-mannose glycans present on various glycoproteins, a three-dimensional (3D) model of the chimera was designed from the crystal structures of recombinant banana lectin (BanLec, Protein Data Bank entry (PDB): 5EXG) and an enhanced green fluorescent protein (eGFP, PDB 4EUL) by applying molecular modeling and molecular mechanics and expressed in Escherichia coli. BanLec-eGFP, produced as a soluble cytosolic protein of about 42 kDa, revealed β-sheets (41%) as the predominant secondary structures, with the emission peak maximum detected at 509 nm (excitation wavelength 488 nm). More than 65% of the primary structure was confirmed by mass spectrometry. Competitive BanLec-eGFP binding to high mannose glycans of the influenza vaccine (Vaxigrip®) was shown in a fluorescence-linked lectin sorbent assay (FLLSA) with monosaccharides (mannose and glucose) and wild type BanLec and H84T BanLec mutant. BanLec-eGFP exhibited binding to mannose residues on different strains of Salmonella in flow cytometry, with especially pronounced binding to a Salmonella Typhi clinical isolate. BanLec-eGFP can be a useful tool for screening high-mannose glycosylation sites on different microorganisms.

scholarly journals Two view NURBS reconstruction based on GACO model

2021 ◽  
Author(s):  
Deepika Saini ◽  
Sanoj Kumar ◽  
Manoj K. Singh ◽  
Musrrat Ali
Keyword(s):  
Optimization Algorithms ◽  
Three Dimensional ◽  
Optimization Procedure ◽  
Least Square ◽  
Ant Colony ◽  
Free Form ◽  
Reconstruction Process ◽  
Nurbs Curve ◽  
Data Points ◽  
Ant Colony Optimization Algorithms

AbstractThe key job here in the presented work is to investigate the performance of Generalized Ant Colony Optimizer (GACO) model in order to evolve the shape of three dimensional free-form Non Uniform Rational B-Spline (NURBS) curve using stereo (two) views. GACO model is a blend of two well known meta-heuristic optimization algorithms known as Simple Ant Colony and Global Ant Colony Optimization algorithms. Basically, the work talks about the solution of NURBS-fitting based reconstruction process. Therefore, GACO model is used to optimize the NURBS parameters (control points and weights) by minimizing the weighted least-square errors between the data points and the fitted NURBS curve. The algorithm is applied by first assuming some pre-fixed values of NURBS parameters. The experiments clearly show that the optimization procedure is a better option in a case where good initial locations of parameters are selected. A detailed experimental analysis is given in support of our algorithm. The implemented error analysis shows that the proposed methodology perform better as compared to the conventional methods.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

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