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MP-T: improving membrane protein alignment for structure prediction

Jamie R. Hill, Charlotte M. Deane
2012 Computer applications in the biosciences : CABIOS  
Results: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment.  ...  Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models.  ...  ACKNOWLEDGEMENT The authors thank Sebastian Kelm for help running the iMembrane and MEDELLER programs, James Dunbar for assistance with Pymol and the members of the Oxford Protein Informatics Group for  ... 
doi:10.1093/bioinformatics/bts640 pmid:23110969 fatcat:sv3kgc6yy5hy7ectfc33okg324

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

Dmitrii M. Nikolaev, Anton Emelyanov, Vitaly M. Boitsov, Maxim S Panov, Mikhail N. Ryazantsev
2017 F1000Research  
Structure. 2013; 21(10): 1735-1742. PubMed Abstract | Publisher Full Text | Free Full Text 10. Hill JR, Deane CM: MP-T: improving membrane protein alignment for structure prediction.  ...  Wu S, Zhang Y: MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins. 2008; 72(2): 547-556.  ...  Two of the alignment methods are specifically constructed for membrane proteins, MP-T 10 and AlignMe 11 , and the third one, MUSTER 12 , gains its quality from evolutionary predictions.  ... 
doi:10.12688/f1000research.10541.1 pmid:28435665 pmcid:PMC5381632 fatcat:3sgux6b7v5dsplerrzf6trh7tu

A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction

Dmitrii M. Nikolaev, Andrey A. Shtyrov, Maxim S. Panov, Adeel Jamal, Oleg B. Chakchir, Vladimir A. Kochemirovsky, Massimo Olivucci, Mikhail N. Ryazantsev
2018 ACS Omega  
For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling.  ...  In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures  ...  of several modern protein structure prediction methodologies (both developed for soluble proteins and membrane-specific protocols).  ... 
doi:10.1021/acsomega.8b00721 pmid:30087916 pmcid:PMC6068592 fatcat:knmdhr3sa5fnpg6mlvso6bjoge

Memoir: template-based structure prediction for membrane proteins

Jean-Paul Ebejer, Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
2013 Nucleic Acids Research  
As a result, for a membrane protein of interest, the much-needed structural information usually comes from a homology model.  ...  Current homology modelling software is optimized for globular proteins, and ignores the constraints that the membrane is known to place on protein structure.  ...  ACKNOWLEDGEMENTS We would like to thank our fellow members of the Oxford Protein Informatics Group for useful discussions.  ... 
doi:10.1093/nar/gkt331 pmid:23640332 pmcid:PMC3692111 fatcat:az47ghyxfrfjbo4s2qz4inizji

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

Dmitrii M. Nikolaev, Anton Emelyanov, Vitaly M. Boitsov, Maxim S Panov, Mikhail N. Ryazantsev
2017 F1000Research  
We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3.  ...  Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level  ...  Two of the alignment methods are specifically constructed for membrane proteins, MP-T 10 and AlignMe 11 , and the third one, MUSTER 12 , gains its quality from evolutionary predictions.  ... 
doi:10.12688/f1000research.10541.2 pmid:28435665 pmcid:PMC5381632 fatcat:z4yzm7meszazzhrhmui2jgyb2q

A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling

Dmitrii M. Nikolaev, Anton Emelyanov, Vitaly M. Boitsov, Maxim S Panov, Mikhail N. Ryazantsev
2017 F1000Research  
We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3.  ...  Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level  ...  The root directory of the supplemental data should include a single clearly written readme.txt file explaining how to access the output structures of each of their homology models.  ... 
doi:10.12688/f1000research.10541.3 pmid:28435665 pmcid:PMC5381632 fatcat:yazlttbehjbrzfkgkcjc7fx2dq

AlignMe—a membrane protein sequence alignment web server

Marcus Stamm, René Staritzbichler, Kamil Khafizov, Lucy R. Forrest
2014 Nucleic Acids Research  
We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe.  ...  These settings utilize different types of inputs: (positionspecific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity  ...  , Garching, Germany for servers and assistance.  ... 
doi:10.1093/nar/gku291 pmid:24753425 pmcid:PMC4086118 fatcat:mwdgbn7phvbgbhx4w6x2toxpfi

Alignment of Helical Membrane Protein Sequences Using AlignMe

Marcus Stamm, René Staritzbichler, Kamil Khafizov, Lucy R. Forrest, Alexandre G. de Brevern
2013 PLoS ONE  
Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments.  ...  Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect  ...  Acknowledgments We thank Dr Jens Meiler for useful discussions, Michael Remmert and Arne Elofsson for help with HHalign and OCTOPUS, respectively, and Dr Jose ´Faraldo-Go ´mez for comments on the manuscript  ... 
doi:10.1371/journal.pone.0057731 pmid:23469223 pmcid:PMC3587630 fatcat:gy6i4bzv2zfg5gu5qzstlbxroy

Computational modeling of membrane proteins

Julia Koehler Leman, Martin B. Ulmschneider, Jeffrey J. Gray
2014 Proteins: Structure, Function, and Bioinformatics  
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure  ...  The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade.  ...  We are also very grateful for the valuable comments from Kalina Hristova and Oliver Beckstein after proofreading the manuscript.  ... 
doi:10.1002/prot.24703 pmid:25355688 pmcid:PMC4270820 fatcat:lk7ku2koqnfi5axp7luxq6e44e

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

Katja Venko, A. Roy Choudhury, Marjana Novič
2017 Computational and Structural Biotechnology Journal  
In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helixhelix interactions, helix  ...  We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase.  ...  MP-T [52] , PRALINE™ [53] , TM-Coffee [54] ) enable promising progress.  ... 
doi:10.1016/j.csbj.2017.01.008 pmid:28228927 pmcid:PMC5312651 fatcat:4ut7l5uvbvektbj5eimfuqgftm

Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors

Stephanie J. Spielman, Keerthana Kumar, Claus O. Wilke
2015 PeerJ  
MP-T: improving membrane protein alignment for structure prediction. Bioinformatics 29(1):54-61 DOI 10.1093/bioinformatics/bts640.  ...  In particular, we have integrated a traditional multiple sequence approach with robust structural domain predictions to ensure that alignment columns accurately capture the highly-conserved GPCR structural  ...  Sedaghat, MD, PhD for suggesting biogenic amine receptor evolution as a worthwhile study system.  ... 
doi:10.7717/peerj.773 pmid:25737813 pmcid:PMC4338800 fatcat:x5zzikvylzfg7pymtk6vppbrhi

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Yarden Golan, Raphael Alhadeff, Fabian Glaser, Assaf Ganoth, Arieh Warshel, Yehuda G. Assaraf, Garegin A. Papoian
2018 PLoS Computational Biology  
Zinc is an essential trace element with 10% of the proteins in the human proteome capable of zinc binding. Thus, zinc deficiency or impairment of zinc homeostasis disrupt key cellular functions.  ...  These computational findings were functionally validated using site-directed mutagenesis of ZnT2 residues predicted to reside along the putative zinc permeation pathway and zinc transport assay.  ...  Briefly, homologous sequences are aligned by MP-T [53] , guided by the membrane information from iMembrane [54] .  ... 
doi:10.1371/journal.pcbi.1006503 fatcat:6efovamy2bdrrl7brv2r77fwve

Three trans-acting regulatory functions control hydrogenase synthesis in Alcaligenes eutrophus

G Eberz, B Friedrich
1991 Journal of Bacteriology  
hydrogenase proteins, although at a reduced level.  ...  HoxA- mutants of A. eutrophus lacked both NAD-reducing soluble hydrogenase and membrane-bound hydrogenase.  ...  ACKNOWLEDGMENTS We thank Marita Feldotte and Angelika Strack for technical assistance and Edward Schwartz for stimulating discussions and critical reading of the manuscript.  ... 
doi:10.1128/jb.173.6.1845-1854.1991 pmid:2001989 pmcid:PMC207712 fatcat:gnvd7kzu5na4zm3j263xxuc3ta

Novel Expansion of Matrix Metalloproteases in the Laboratory Axolotl (Ambystoma mexicanum) and Other Salamander Species

Nour Al Haj Baddar, Nataliya Timoshevskaya, Jeramiah J. Smith, Houfu Guo, S. Randal Voss
2021 Frontiers in Ecology and Evolution  
Matrix metalloprotease (MMP) genes encode endopeptidases that cleave protein components of the extracellular matrix (ECM) as well as non-ECM proteins.  ...  Our analysis sets the stage for comparative studies to understand why MMPs expanded uniquely within salamanders.  ...  The predicted 3D structure of the aligned evolved novel insertions.  ... 
doi:10.3389/fevo.2021.786263 fatcat:u34beuifknautf5t63ngxrom4y

Learning to Fold Proteins Using Energy Landscape Theory [article]

N.P. Schafer, B.L. Kim, W. Zheng, P.G. Wolynes
2013 arXiv   pre-print
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using  ...  Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes  ...  One such example is that of membrane proteins.  ... 
arXiv:1312.7283v1 fatcat:5qucheladjhkfd2m7xmq3cdbvy
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