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Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

Rita Pancsa, Mihaly Varadi, Peter Tompa, Wim F. Vranken
2015 Nucleic Acids Research  
Start2Fold is an openly accessible database (http://start2fold.eu) of carefully curated hydrogen/deuterium exchange (HDX) data extracted from the literature that is open for new submissions from the community  ...  Since the 1950's, solvent exchange-based methods have been the most powerful experimental means to obtain information on the folding and stability of proteins.  ...  Among these approaches, hydrogen/deuterium exchange (HDX) techniques are the most widely used (1, 6) ; they are based on the notion that, for a given residue, the rate of proton exchange between its backbone  ... 
doi:10.1093/nar/gkv1185 pmid:26582925 pmcid:PMC4702845 fatcat:vuslv4yrefhitidsq3hd2nt3j4

Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook

Minh H. Tran, Clara T. Schoeder, Kevin L. Schey, Jens Meiler
2022 Frontiers in Immunology  
A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS).  ...  Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking.  ...  The development of an HDX-NMR incorporated scoring system was made possible thanks to a large HDX-NMR dataset on protein folding and stability available via the Start2Fold database (130, 133) .  ... 
doi:10.3389/fimmu.2022.859964 pmid:35720345 pmcid:PMC9204306 fatcat:ijlvxd47kfd3lod6b4zs4xjrb4

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases

Sebastian Bittrich, Michael Schroeder, Dirk Labudde, Yaakov Koby Levy
2018 PLoS ONE  
The Start2Fold database is used to investigate whether this separation of EFR and functional residues can be observed for other proteins.  ...  Without external influence, many proteins fold into their native structure, and a small number of Early Folding Residues (EFR) have previously been shown to initiate the formation of secondary structure  ...  Furthermore, the authors acknowledge scientific discussion and proofreading of the manuscript by Florian Kaiser, Christoph Leberecht, Sebastian Salentin, and Alexander Eisold.  ... 
doi:10.1371/journal.pone.0206369 fatcat:5zw4mzqbk5bqfeeaxn6of5ul4e

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins

Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F. Vranken
2017 Scientific Reports  
The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities  ...  To obtain a more accurate picture of such 'early folding' residues in proteins, we recently created the Start2Fold database, which collects data from pulsed labelling and related HDX experiments 14 .  ...  There is a crucial experimental difference with native exchange HDX experiments, where residues protected from solvent in the native folded state are identified: the hydrogen/ deuterium exchange regime  ... 
doi:10.1038/s41598-017-08366-3 pmid:28821744 pmcid:PMC5562875 fatcat:d3q23dds6fcoxefyqt5aaeyto4

The 2016 database issue ofNucleic Acids Researchand an updated molecular biology database collection

Daniel J. Rigden, Xosé M. Fernández-Suárez, Michael Y. Galperin
2016 Nucleic Acids Research  
The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling.  ...  A further six papers present updated databases of various antimicrobial and anticancer peptides.  ...  ACKNOWLEDGEMENTS We thank NAR Editorial Administrator Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their great efforts in compiling this  ... 
doi:10.1093/nar/gkv1356 pmid:26740669 pmcid:PMC4702933 fatcat:3bkogosuu5g4lduv7ne5i6h6qi

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases [article]

Sebastian Bittrich, Michael Schroeder, Dirk Labudde
2018 bioRxiv   pre-print
A dataset of 30 proteins and 3,337 residues provided by the Start2Fold database was analyzed. Proteins were represented as residue graphs in order to analyze topological descriptors of EFR.  ...  Without external influence, most proteins fold into their correct structure, and a small number of Early Folding Residues (EFR) have previously been shown to initiate the formation of secondary structure  ...  Acknowledgments 623 The authors thank Florian Kaiser, Christoph Leberecht, Sebastian Salentin, and 624 Alexander Eisold for scientific discussions and/or proofreading the manuscript.  ... 
doi:10.1101/290627 fatcat:hhlbabvnkvhyfpnjooln4ynyta

StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map

Sebastian Bittrich, Michael Schroeder, Dirk Labudde
2019 Scientific Reports  
Protein folding and structure prediction are two sides of the same coin.  ...  We employ the proposed SR score to demonstrate that folding initiation and structure stabilization are subprocesses realized by distinct sets of residues.  ...  The findings described in this paper have been previously published in the thesis "Understanding the Structural and Functional Importance of Early Folding Residues in Protein Structures" by S.B.  ... 
doi:10.1038/s41598-019-55047-4 pmid:31811259 pmcid:PMC6898053 fatcat:lmqmeccdvve4zlmupdezv2np2u

StructureDistiller: Structural relevance scoring increases resilience of contact maps to false positive predictions [article]

Sebastian Bittrich, Michael Schroeder, Dirk Labudde
2019 bioRxiv   pre-print
Protein folding and structure prediction are two sides of the same coin.  ...  Furthermore, knowledge of the most relevant contacts significantly increases reconstruction fidelity on sparse contact maps by 0.4 Å.  ...  Acknowledgements 669 The authors thank Jose Duarte, Christoph Leberecht, Sarah Krautwurst, and Florian Kaiser 670 for scientific discussions and/or proofreading of the manuscript.  ... 
doi:10.1101/697839 fatcat:grywvj5s75flnn76eq5a55az7e

Application of an interpretable classification model on Early Folding Residues during protein folding

Sebastian Bittrich, Marika Kaden, Christoph Leberecht, Florian Kaiser, Thomas Villmann, Dirk Labudde
2019 BioData Mining  
The feasibility of GMLVQ is demonstrated on a dataset of Early Folding Residues (EFR) that have been shown to initiate and guide the protein folding process.  ...  allow for a fine-grained interpretation of the data.  ...  Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Received: 6 August 2018 Accepted: 20 November 2018  ... 
doi:10.1186/s13040-018-0188-2 pmid:30627219 pmcid:PMC6321665 fatcat:2yfvdn3qqrc3nplvrlsoqkmmym

Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index

Gabriele Orlando, Daniele Raimondi, Wim F. Vranken
2019 Nature Communications  
Chemical shifts (CS) are determined from NMR experiments and represent the resonance frequency of the spin of atoms in a magnetic field.  ...  They contain a mixture of information, encompassing the in-solution conformations a protein adopts, as well as the movements it performs.  ...  The Start2Fold database contains information about which residues in proteins are the first to start folding, when the proteins folds from a statistical chain state, as studied by hydrogen/deuterium exchange  ... 
doi:10.1038/s41467-019-10322-w pmid:31175284 pmcid:PMC6555786 fatcat:wprzrzsogra2xo6fqpxc7g3zre