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Conformational dynamics of SNARE recycling mediated by NSF. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0r240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Conformational Dynamics of SNARE Proteins during NSF‐Mediated Disassembly. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Processing simultaneously collected MAD data from two closely spaced (90 eV) wavelengths measured at an X-ray free-electron laser. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319097617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mechanistic Insights into NSF Mediated SNARE Complex Disassembly. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Structure Refinement at Low-resolution: Strategies and Validation. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314085179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the refinement of macromolecular structures at low resolution (worse than 3.5 A) over-fitting becomes a serious problem since the number of degrees of freedom (i.a. atomic coordinates) is often much larger than the number of experimental observables (number of unique reflections). Applying additional restraints help to reduce the effective number of degrees of freedom but will necessarily limit the conformational freedom of the structure during the refinement. These restraints could therefore prevent finding the optimum solution, which means the choice of restraints is important. Strategies will be presented to choose such restraints. For example the Deformable Elastic Network (DEN) approach adapts restraints automatically, on the one hand to allow for relevant conformational changes to occur and on the other hand to keep those degrees of freedom well restrained for which no experimental data are available [1]. Some recent examples [2] of low-resolution structures will be presented including the refinement of the chaperonin TRiC in a closed (3.8 A) and open (5.5 A) conformation [3]. This example also shows that new validation tools might be important at low resolution in a addition to traditional cross-validation. For example exhaustive sampling of alternative models can provide additional information on the reliability and statistical significance of the optimum structure solution.
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New Insights into the Molecular Mechanism of Calcium-Triggered Synaptic Vesicle Fusion. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Reconstitution of Calcium-Triggered Synaptic Vesicle Fusion. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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The Structure of Nucleotide Pyrophosphatase/ Phosphodiesterase and Implications for Enzyme Evolution in the Alkaline Phosphatase Superfamily. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a477-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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