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Model quality assessment for membrane proteins

Arjun Ray, Erik Lindahl, Björn Wallner
2010 Computer applications in the biosciences : CABIOS  
Motivation: Learning-based model quality assessment programs have been quite successful at discriminating between high-and lowquality protein structures.  ...  Results: Our new ProQM method uses a support vector machine with a combination of general and membrane-protein-specific features.  ...  In summary, we believe ProQM provides a highly useful improvement for quality assessment of membrane protein structures, in particular due to its local scoring.  ... 
doi:10.1093/bioinformatics/btq581 pmid:20947525 fatcat:5wmmojkwyzh6pndwezjbrq6djm

Membrane Insertion of a Voltage-Sensor Helix

Chze Ling Wee, Mark Sansom
2010 Biophysical Journal  
Predicted outer membrane protein L (OmpL) from Salmonella typhimurium LT2, was tested as a model for validating the prediction method.  ...  Recombinant OmpL localizes to the outer membrane when expressed in Escherichia coli; OmpL has b-sheet-rich secondary structure with stable tertiary contacts in the presence of either detergent micelles  ...  It was shown that MD stereochemical profiles can be used to distinguish between models constructed based on high quality template structures, models constructed based on a low quality template structures  ... 
doi:10.1016/j.bpj.2009.12.3532 fatcat:dtjqcutcwvgedg44dewltbinee

Prediction of transmembrane helix orientation in polytopic membrane proteins

Larisa Adamian, Jie Liang
2006 BMC Structural Biology  
LIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins.  ...  We present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins.  ...  Our method can be used for the prediction of helix orientation in the ab initio modeling of polytopic membrane proteins.  ... 
doi:10.1186/1472-6807-6-13 pmid:16792816 pmcid:PMC1540425 fatcat:xkld5tynfjcgbmhyzysvunu4lu

Grafted biomembranes containing membrane proteins – the case of the leucine transporter

Vivien Jagalski, Robert D. Barker, Mikkel B. Thygesen, Kamil Gotfryd, Mie B. Krüger, Lei Shi, Selma Maric, Nicolas Bovet, Martine Moulin, Michael Haertlein, Thomas Günther Pomorski, Claus J. Loland (+1 others)
2015 Soft Matter  
Together neutron reflection and molecular dynamics simulation offer a powerful tool to study the membrane protein structure in native-like environment.  ...  We gratefully acknowledge the access to the Deuteration Laboratory (D-Lab) PSB platform within ILL's Life Sciences Group.  ...  VJ and MC also thank funding from Plant Power: Light-driven synthesis of complex terpenoids using cytochrome P450s (12-131834) funded by  ... 
doi:10.1039/c5sm01490e pmid:26325086 fatcat:zbikdrtubfcdlpchonea2safia

Benchmarking Collective Motion Predictions of Elastic Network Models

Edvin Fuglebakk, Nathalie Reuter, Konrad Hinsen
2014 Biophysical Journal  
approaches, we present a graphics-processing unit (GPU)-optimized coarsegrained Go-type MD simulation approach for protein-nanoparticle interactions, the first in the field.  ...  Consistent with the CD spectra, we observed a decrease in a-helices coupled with an increase in b-sheets in apolipoprotein upon biocorona formation.  ...  ; it provides numerous physically meaningful hydrogen bonding connections; and it provides correct embedding of membrane proteins in lipid bilayer membranes.  ... 
doi:10.1016/j.bpj.2013.11.2618 fatcat:dzizy7tog5c2ha3lhurasuzlsm

Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

Timothy Nugent, David T. Jones, Arne Elofsson
2010 PLoS Computational Biology  
Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable  ...  Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy.  ...  Another method calculated amino acid substitution tables for residues in membrane proteins where the side chain was accessible to lipid.  ... 
doi:10.1371/journal.pcbi.1000714 pmid:20333233 pmcid:PMC2841610 fatcat:e2jwbyh2ivghhihb7dputw2ene

PRIMO-M: An Extension of the Coarse-Grained Force Field Primo to the Membrane Environment

Parimal Kar, Michael Feig
2014 Biophysical Journal  
approaches, we present a graphics-processing unit (GPU)-optimized coarsegrained Go-type MD simulation approach for protein-nanoparticle interactions, the first in the field.  ...  Consistent with the CD spectra, we observed a decrease in a-helices coupled with an increase in b-sheets in apolipoprotein upon biocorona formation.  ...  ; it provides numerous physically meaningful hydrogen bonding connections; and it provides correct embedding of membrane proteins in lipid bilayer membranes.  ... 
doi:10.1016/j.bpj.2013.11.2619 fatcat:a7zu47vf3jhf3gz4ywd3qkrwvu

NMR-Restrained Protein Structure Calculations in Implicit Environment

Ye Tian, Charles Schwieters, Stanley J. Opella, Francesca M. Marassi
2014 Biophysical Journal  
approaches, we present a graphics-processing unit (GPU)-optimized coarsegrained Go-type MD simulation approach for protein-nanoparticle interactions, the first in the field.  ...  Consistent with the CD spectra, we observed a decrease in a-helices coupled with an increase in b-sheets in apolipoprotein upon biocorona formation.  ...  ; it provides numerous physically meaningful hydrogen bonding connections; and it provides correct embedding of membrane proteins in lipid bilayer membranes.  ... 
doi:10.1016/j.bpj.2013.11.2617 fatcat:4ziyexpxb5abbnchjqjf6wumki

Biophysical Insights of Neutral and Non-Neutral Sequence Variants in the Human Proteome

Brandon M. Butler, Sudhir Kumar, Sefika B. Ozkan
2014 Biophysical Journal  
approaches, we present a graphics-processing unit (GPU)-optimized coarsegrained Go-type MD simulation approach for protein-nanoparticle interactions, the first in the field.  ...  Consistent with the CD spectra, we observed a decrease in a-helices coupled with an increase in b-sheets in apolipoprotein upon biocorona formation.  ...  ; it provides numerous physically meaningful hydrogen bonding connections; and it provides correct embedding of membrane proteins in lipid bilayer membranes.  ... 
doi:10.1016/j.bpj.2013.11.2616 fatcat:25pjiknnbrbofea3iotvnxoyim

Structure Evaluation of IroN for Designing a Vaccine against Escherichia Coli, an In Silico Approach

Fateme Sefid, Roghayyeh Baghban, Zahra Payandeh, Bahman Khalesi, Mohammad Mahmoudi Gomari, Department of Medical Genetics, Shahid Sadoughi University of Medical Science, Yazd, Iran, Department of Biology, Science and Art University, Yazd, Iran, Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran, Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extention Organization (AREEO), Karaj, Iran, Department of Medical Biotechnology, Faculty of Paramedical, Iran University of Medical Science, Tehran, Iran
2019 Journal of Medical Microbiology and Infectious Diseases  
The obtained models were all taken for further quality assessment. Models Quality Assessment.  ...  Model quality assessment using Ramachandran plot before and after refinement for IroN models Protein-Ligand Binding Site Prediction.  ... 
doi:10.29252/jommid.7.4.93 fatcat:p2oqfzhbavhrfozsmgdauialcm

Diverse scientific benchmarks for implicit membrane energy functions [article]

Rebecca F. Alford, Jeffrey J. Gray
2020 bioRxiv   pre-print
Yet, energy functions for membrane proteins lag behind due to sparse and low-quality data, leading to overfit tools.  ...  Over the past 20 years, progress in each area has advanced soluble protein energy functions.  ...  ) to make the tests accessible to all membrane protein modeling developers.  ... 
doi:10.1101/2020.06.23.168021 fatcat:yavsvd7dlnei5cl3ud7tp5xiyy

Anisotropic Solvent Model of the Lipid Bilayer. 2. Energetics of Insertion of Small Molecules, Peptides, and Proteins in Membranes

Andrei L. Lomize, Irina D. Pogozheva, Henry I Mosberg
2011 Journal of Chemical Information and Modeling  
In this study, we extended this model to quantify the energetics of proteinÀlipid interactions in artificial lipid bilayers and natural biological membranes.  ...  post-translational insertion in membranes of transmembrane R-helical 5À8 or β-barrel proteins, 9 membraneassociated peptides, toxins, and peripheral proteins. 10 Modulation of lipids influences spatial  ...  We assessed the water concentrations in the "mid-polar" and the central regions of different biological membranes by fitting the theoretically predicted and statistical energy profiles for Trp and Tyr  ... 
doi:10.1021/ci200020k pmid:21438606 pmcid:PMC3091260 fatcat:3goeeyt4zvcxdhyncxnaskq2i4

Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains

Shaneen M. Singh, Diana Murray
2003 Protein Science  
lipid-binding site identified in the PLC␦1-PH structure.  ...  In particular, our calculations predict that (1) members from each of the four PLC classes exhibit strikingly different electrostatic profiles than those ordinarily observed for PH domains in general,  ...  The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1110/ps.0358803 pmid:12930993 pmcid:PMC2323991 fatcat:7wruhs3tibd7lav3fo2v7fmyzq

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

Oriol Gallego, Matthew J Betts, Jelena Gvozdenovic-Jeremic, Kenji Maeda, Christian Matetzki, Carmen Aguilar-Gurrieri, Pedro Beltran-Alvarez, Stefan Bonn, Carlos Fernández-Tornero, Lars Juhl Jensen, Michael Kuhn, Jamie Trott (+6 others)
2010 Molecular Systems Biology  
We used arrays of 56 metabolites to measure lipid-binding fingerprints of 172 proteins, including 91 with predicted lipid-binding domains.  ...  Protein-metabolite networks are central to biological systems, but are incompletely understood. Here, we report a screen to catalog protein-lipid interactions in yeast.  ...  (A) Summary of the two reference data sets and strategies used to assess quality.  ... 
doi:10.1038/msb.2010.87 pmid:21119626 pmcid:PMC3010107 fatcat:blxvje6p6rg4lmqwpryjb6dezm

The cytosolic domain of T-cell receptor ζ associates with membranes in a dynamic equilibrium and deeply penetrates the bilayer

Kerstin Zimmermann, Rebecca Eells, Frank Heinrich, Stefanie Rintoul, Brian Josey, Prabhanshu Shekhar, Mathias Lösche, Lawrence J. Stern
2017 Journal of Biological Chemistry  
Interactions between lipid bilayers and the membrane-proximal regions of membrane-associated proteins play important roles in regulating membrane protein structure and function.  ...  Here, using surface plasmon resonance and neutron reflection, we characterized the interaction of cyt with planar lipid bilayers containing mixtures of acidic and neutral lipids.  ...  The setup allows for simultaneous SPR and electrochemical impedance spectroscopy (EIS) measurements, which are used to assess the quality of the stBLMs before and after protein is introduced.  ... 
doi:10.1074/jbc.m117.794370 pmid:28893902 fatcat:hffgljvnujccxhpgik7tdf5f6m
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