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Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins

Wei Tian, Meishan Lin, Hammad Naveed, Jie Liang, Anna Tramontano
2017 Bioinformatics  
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

Hammad Naveed, Jie Liang
2014 Current pharmaceutical design  
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

Xiao Zhu, Pedro Lopes, Jihyun Shim, Alexander D. MacKerell
2011 Biophysical Journal  
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

Eva Darian, Vipin Jain, Bongsup Cho, Alexander D. MacKerell
2011 Biophysical Journal  
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

Rodolfo Briones, Saskia Villinger, Vytautas Gapsys, Ulrich Zachariae, Giller Karin, Christian Griesinger, Bert de Groot, Markus Zweckstetter
2011 Biophysical Journal  
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

Wei Zhao, Valentina Corradi, Peter Tieleman
2011 Biophysical Journal  
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

Xibing He, Wataru Shinoda, Russell Devane, Olgun Guvench, Kelly L. Anderson, Alexander D. MacKerell, Michael L. Klein
2011 Biophysical Journal  
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

Kethika Kulleperuma, John Holyoake, Régis Pomès
2011 Biophysical Journal  
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

Zhijun Li, Jun Gao, Vagmita Pabuwal
2011 Biophysical Journal  
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

James C. Gumbart, Christophe Chipot, Klaus Schulten
2011 Biophysical Journal  
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

Hiroaki Komatsu, Paul H. Axelsen
2011 Biophysical Journal  
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

Amit Kumar, Rebekah L. Rice, Pritesh Patel, Lea C. Paslay, Dipti singh, Ewa A. Bienkiewicz, Sarah E. Morgan, Vijayaraghavan Rangachari
2011 Biophysical Journal  
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]

M. Pirtskhalava, B. Vishnepolsky, M. Grigolava
2013 arXiv   pre-print
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

A Soltani Shirazi, O Azizi, N Bolourchi, Sh Aghamohammad, F Badmasti
2017 Vaccine Research  
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

Timothy Nugent, David T Jones
2013 BMC Bioinformatics  
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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