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Pancsa R, Raimondi D, Cilia E, Vranken WF. Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity. Biophys J 2017; 110:572-583. [PMID: 26840723 DOI: 10.1016/j.bpj.2015.12.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 01/20/2023] Open
Abstract
Protein folding is in its early stages largely determined by the protein sequence and complex local interactions between amino acids, resulting in lower energy conformations that provide the context for further folding into the native state. We compiled a comprehensive data set of early folding residues based on pulsed labeling hydrogen deuterium exchange experiments. These early folding residues have corresponding higher backbone rigidity as predicted by DynaMine from sequence, an effect also present when accounting for the secondary structures in the folded protein. We then show that the amino acids involved in early folding events are not more conserved than others, but rather, early folding fragments and the secondary structure elements they are part of show a clear trend toward conserving a rigid backbone. We therefore propose that backbone rigidity is a fundamental physical feature conserved by proteins that can provide important insights into their folding mechanisms and stability.
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Affiliation(s)
- Rita Pancsa
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniele Raimondi
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elisa Cilia
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
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Pancsa R, Varadi M, Tompa P, Vranken WF. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res 2015; 44:D429-34. [PMID: 26582925 PMCID: PMC4702845 DOI: 10.1093/nar/gkv1185] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/24/2015] [Indexed: 01/02/2023] Open
Abstract
Proteins fulfil a wide range of tasks in cells; understanding how they fold into complex three-dimensional (3D) structures and how these structures remain stable while retaining sufficient dynamics for functionality is essential for the interpretation of overall protein behaviour. 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. Considerable expertise and care were required to obtain the resulting datasets, which, despite their importance and intrinsic value, have never been collected, curated and classified. 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. The database entries contain (i) information on the proteins investigated and the underlying experimental procedures and (ii) the classification of the residues based on their exchange protection levels, also allowing for the instant visualization of the relevant residue groups on the 3D structures of the corresponding proteins. By providing a clear hierarchical framework for the easy sharing, comparison and (re-)interpretation of HDX data, Start2Fold intends to promote a better understanding of how the protein sequence encodes folding and structure as well as the development of new computational methods predicting protein folding and stability.
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Affiliation(s)
- Rita Pancsa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium
| | - Mihaly Varadi
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium
| | - Peter Tompa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium Interuniversity Institute of Bioinformatics in Brussels (IB), ULB-VUB, Brussels 1050, Belgium Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1113, Hungary
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium Interuniversity Institute of Bioinformatics in Brussels (IB), ULB-VUB, Brussels 1050, Belgium
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Magazù S, Migliardo F, Benedetto A, Vertessy B. Protein dynamics by neutron scattering: The protein dynamical transition and the fragile-to-strong dynamical crossover in hydrated lysozyme. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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