The state of the art of membrane protein structure prediction: from sequence to 3D structure

Membrane proteins constitute a very large set of yet-to-be characterized proteins mediating all the relevant life-related functions both in prokaryotes and eukaryotes. Estimates are suggesting that in whole genomes the content of this protein type may vary from 10 to 40% of the whole proteome, depending on the organism.

[1]  J Deisenhofer,et al.  X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. , 1984, Journal of molecular biology.

[2]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.

[3]  L. Brooks,et al.  A DNA polymorphism discovery resource for research on human genetic variation. , 1998, Genome research.

[4]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[5]  R. Casadio,et al.  A 3D model of the voltage‐dependent anion channel (VDAC) , 2002, FEBS letters.

[6]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[7]  S. Henikoff,et al.  Accounting for human polymorphisms predicted to affect protein function. , 2002, Genome research.

[8]  Piero Fariselli,et al.  A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins , 2002, ISMB.

[9]  Piero Fariselli,et al.  MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments , 2003, Bioinform..

[10]  R. Casadio,et al.  Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[11]  Piero Fariselli,et al.  In silico prediction of the structure of membrane proteins: Is it feasible? , 2003, Briefings Bioinform..

[12]  Piero Fariselli,et al.  SPEPlip: the detection of signal peptide and lipoprotein cleavage sites , 2003, Bioinform..

[13]  Piero Fariselli,et al.  An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins , 2003, ISMB.

[14]  J. Bell.  Predicting disease using genomics , 2004, Nature.

[15]  R. Casadio,et al.  Functional Characterization of a Second Porin Isoform in Drosophila melanogaster , 2004, Journal of Biological Chemistry.

[16]  Stavros J. Hamodrakas,et al.  Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method , 2005, BMC Bioinformatics.

[17]  A. Elofsson,et al.  Best α‐helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information , 2004 .

[18]  Andreas Bernsel,et al.  Improved membrane protein topology prediction by domain assignments , 2005, Protein science : a publication of the Protein Society.

[19]  R. Casadio,et al.  Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study , 2005, Molecular membrane biology.

[20]  Piero Fariselli,et al.  TRAMPLE: the transmembrane protein labelling environment , 2005, Nucleic Acids Res..

[21]  Piero Fariselli,et al.  A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins , 2005, BMC Bioinformatics.

[22]  G. von Heijne,et al.  Materials and Methods Figs. S1 to S3 References and Notes Global Topology Analysis of the Escherichia Coli Inner Membrane Proteome , 2022 .

[23]  Johan Nilsson,et al.  Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes , 2005, Proteins.

[24]  Emidio Capriotti,et al.  Bioinformatics Original Paper Predicting the Insurgence of Human Genetic Diseases Associated to Single Point Protein Mutations with Support Vector Machines and Evolutionary Information , 2022 .

[25]  Arne Elofsson,et al.  PONGO: a web server for multiple predictions of all-alpha transmembrane proteins , 2006, Nucleic Acids Res..

[26]  G. von Heijne,et al.  A global topology map of the Saccharomyces cerevisiae membrane proteome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Marialuisa Pellegrini-Calace,et al.  Towards genome-scale structure prediction for transmembrane proteins , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[28]  Rita Casadio,et al.  New Escherichia coli outer membrane proteins identified through prediction and experimental verification , 2006, Protein science : a publication of the Protein Society.

[29]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[30]  Marco Punta,et al.  Membrane protein prediction methods. , 2007, Methods.

[31]  G. von Heijne,et al.  Membrane protein structure: prediction versus reality. , 2007, Annual review of biochemistry.

[32]  David T. Jones,et al.  Improving the accuracy of transmembrane protein topology prediction using evolutionary information , 2007, Bioinform..

[33]  R. Casadio,et al.  Thinking the impossible: how to solve the protein folding problem with and without homologous structures and more. , 2007, Methods in molecular biology.