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Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins
2017
Bioinformatics
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Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane ...
Motivation: Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. ...
Materials The PDB codes of the TMBs used in this study can be found in the Supplementary Information.
Funding This work was supported by NIH grant GM079804. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btx053
pmid:28158457
pmcid:PMC5860226
fatcat:tml5ykfasrewngygzcqzn54xjy
Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins
2014
Current pharmaceutical design
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We discuss the emerging concept of weakly stable regions in β-barrel membrane proteins, computational methods to identify these regions and mechanisms adopted by β-barrel membrane proteins in nature to ...
We briefly discuss recent progress in computational characterization of the sequence and structural properties of β-barrel membrane properties. ...
HN is supported by the Fulbright Fellowship and the Higher Education Commission of Pakistan. ...
doi:10.2174/13816128113199990071
pmid:23713778
pmcid:PMC4127314
fatcat:d3e72wqyvnestbbhiscppyup7i
Analysis of Amino Acid Sidechain Chi1, Chi2 Conformational Properties Using Quantum Mechanical and Experimental Crystallographic Survey Data
2011
Biophysical Journal
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The free energy landscape thus calculated clarifies the role of the calcium ion in the enzyme activity. ...
Comprehensive conformational sampling of the disordered loop has been performed to elucidate how flexible the disordered loop in the peptide free form is and how the peptide and calcium binding affect ...
Amino acid side chain flexibility is an important property that influences the side-chain interactions in proteins as well as protein stability. ...
doi:10.1016/j.bpj.2010.12.1010
fatcat:nk22iya5u5bnpit4ismnbjbj3m
Sequence Dependent Free Energy Estimates of Base Opening in Arylamine-Induced DNA-Adducts
2011
Biophysical Journal
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The free energy landscape thus calculated clarifies the role of the calcium ion in the enzyme activity. ...
Comprehensive conformational sampling of the disordered loop has been performed to elucidate how flexible the disordered loop in the peptide free form is and how the peptide and calcium binding affect ...
Amino acid side chain flexibility is an important property that influences the side-chain interactions in proteins as well as protein stability. ...
doi:10.1016/j.bpj.2010.12.1011
fatcat:lscksxof7fbfhfphf77a3v7fra
Lipid Protein Interactions and Dynamical Properties of VDAC 1 channel
2011
Biophysical Journal
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The free energy landscape thus calculated clarifies the role of the calcium ion in the enzyme activity. ...
Comprehensive conformational sampling of the disordered loop has been performed to elucidate how flexible the disordered loop in the peptide free form is and how the peptide and calcium binding affect ...
Amino acid side chain flexibility is an important property that influences the side-chain interactions in proteins as well as protein stability. ...
doi:10.1016/j.bpj.2010.12.1008
fatcat:f3byrk2bynaipbssrcdifbp7fy
Molecular Dynamics Simulations of Anionic Lipid Bilayers in Presence of Calcium Ions
2011
Biophysical Journal
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The free energy landscape thus calculated clarifies the role of the calcium ion in the enzyme activity. ...
Comprehensive conformational sampling of the disordered loop has been performed to elucidate how flexible the disordered loop in the peptide free form is and how the peptide and calcium binding affect ...
Amino acid side chain flexibility is an important property that influences the side-chain interactions in proteins as well as protein stability. ...
doi:10.1016/j.bpj.2010.12.1007
fatcat:x4liz7b3hzd7bjpbhtwuwntlxy
Development of a Coarse-Grained Model for the Surfactant Family of Linear Alkylbenzene Sulfonates
2011
Biophysical Journal
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The free energy landscape thus calculated clarifies the role of the calcium ion in the enzyme activity. ...
Comprehensive conformational sampling of the disordered loop has been performed to elucidate how flexible the disordered loop in the peptide free form is and how the peptide and calcium binding affect ...
Amino acid side chain flexibility is an important property that influences the side-chain interactions in proteins as well as protein stability. ...
doi:10.1016/j.bpj.2010.12.1009
fatcat:rvhzmaymqzdp3dr5zpclio257e
A general and Efficient All-Atom Simulation Method to Determine the Equilibrium Orientation of Transmembrane Proteins in Membranes
2011
Biophysical Journal
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Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
Experiments and simulations measuring the free energy of insertion for various amino acids are in disagreement, with the former finding a much narrower range than the latter. ...
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
doi:10.1016/j.bpj.2010.12.1323
fatcat:v4qpnbwllzcp7dc3mphrlg4v6a
Analyzing Inter-Residue Interactions for Structure Modeling of Helical Membrane Proteins
2011
Biophysical Journal
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Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
Experiments and simulations measuring the free energy of insertion for various amino acids are in disagreement, with the former finding a much narrower range than the latter. ...
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
doi:10.1016/j.bpj.2010.12.1321
fatcat:q6d6gff64vhqjp56qevi4bn37i
Protein Folding and Membrane Insertion via the Protein Translocon
2011
Biophysical Journal
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Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
Experiments and simulations measuring the free energy of insertion for various amino acids are in disagreement, with the former finding a much narrower range than the latter. ...
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
doi:10.1016/j.bpj.2010.12.1322
fatcat:gxfmxzfsvvf3heobp6piwizgyi
Topology of His Residues in Amyloid β Protein Fibrils
2011
Biophysical Journal
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
Experiments and simulations measuring the free energy of insertion for various amino acids are in disagreement, with the former finding a much narrower range than the latter. ...
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
doi:10.1016/j.bpj.2010.12.1320
fatcat:zhjmsefn4zcullitape2dr34pe
Non-Esterified Fatty Acids (NEFAs) Generate Distinct Aβ42 Oligomers via Two Distinct Aggregation Pathways
2011
Biophysical Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
Experiments and simulations measuring the free energy of insertion for various amino acids are in disagreement, with the former finding a much narrower range than the latter. ...
Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a helical ...
doi:10.1016/j.bpj.2010.12.1319
fatcat:xhgww5kagzejrpiyqneonvurbu
Transmembrane and Antimicrobial Peptides. Hydrophobicity, Amphiphilicity and Propensity to Aggregation
[article]
2013
arXiv
pre-print
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For some kind of peptides such characteristics as hydrophobicity, amphiphilicity and aggregation bias determines their ability to compose transmembrane domain of the membrane protein, whilst for others ...
The efficient designing of the new antimicrobials on the basis of antimicrobial peptides requires comprehensive knowledge on those general physical-chemical characteristics which allow to differ antimicrobial ...
Acknowledgement The designated work has fulfilled by financial support of the CNRS / SRNSF Grant No 09/10. ...
arXiv:1307.6160v1
fatcat:ylg2af4si5bivin4kqcbfv4rsu
Comparative in silico analyses of proteins involved in serum resistance as promising vaccine candidates against Acinetobacter baumannii
2017
Vaccine Research
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Our aim in this project was in silico analyses of A. baumannii proteins involved in serum resistance which could potentially be used as efficient vaccines. ...
The numbers of immunogenic linear and conformational epitopes with high score (P ≥ 0.6), extracted from beta-barrel of AbOmpA were 6 and 4; whereas these values for PKF were 10 and 4, respectively. ...
ACKNOWLEDGEMENT The authors would like to thank the personnel in Department of Bacteriology of Pasture Institute of Iran for their help. ...
doi:10.29252/vacres.4.3.4.64
fatcat:oomj4ubzhzgdlgricvmhnutcfy
Membrane protein orientation and refinement using a knowledge-based statistical potential
2013
BMC Bioinformatics
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Recent increases in the number of deposited membrane protein crystal structures necessitate the use of automated computational tools to position them within the lipid bilayer. ...
, and demonstrate its use in positioning proteins in membranes, refinement of membrane protein models and in decoy discrimination. ...
of all amino acids found at depth z. ...
doi:10.1186/1471-2105-14-276
pmid:24047460
pmcid:PMC3852961
fatcat:ckvleqfpnff4lpf3srydt2y3y4
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