Literature DB >> 27862777

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

Wilfred F van Gunsteren1, Jane R Allison2,3,4, Xavier Daura5,6, Jožica Dolenc1, Niels Hansen7, Alan E Mark8, Chris Oostenbrink9, Victor H Rusu1, Lorna J Smith10.   

Abstract

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Qexp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Qexp , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Qexp , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.
© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  ambiguities; averaging; biomolecular structure determination; errors; experimental data

Mesh:

Substances:

Year:  2016        PMID: 27862777     DOI: 10.1002/anie.201601828

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN: 1433-7851            Impact factor:   15.336


  6 in total

1.  Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.

Authors:  Aysegül Turupcu; Matthias Diem; Lorna J Smith; Chris Oostenbrink
Journal:  Chemphyschem       Date:  2019-05-06       Impact factor: 3.520

2.  An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose.

Authors:  Aysegul Turupcu; Alice M Bowen; Alexandre Di Paolo; André Matagne; Chris Oostenbrink; Christina Redfield; Lorna J Smith
Journal:  Proteins       Date:  2019-07-26

Review 3.  Recent Developments in Data-Assisted Modeling of Flexible Proteins.

Authors:  Cezary Czaplewski; Zhou Gong; Emilia A Lubecka; Kai Xue; Chun Tang; Adam Liwo
Journal:  Front Mol Biosci       Date:  2021-12-24

4.  Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.

Authors:  Maria Pechlaner; Wilfred F van Gunsteren; Niels Hansen; Lorna J Smith
Journal:  Eur Biophys J       Date:  2022-03-18       Impact factor: 2.095

5.  Molecular Conformations of Di-, Tri-, and Tetra-α-(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations.

Authors:  Aysegül Turupcu; Markus Blaukopf; Paul Kosma; Chris Oostenbrink
Journal:  Int J Mol Sci       Date:  2019-12-19       Impact factor: 6.208

6.  On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.

Authors:  Lorna J Smith; Wilfred F van Gunsteren; Niels Hansen
Journal:  Chembiochem       Date:  2020-12-14       Impact factor: 3.164

  6 in total

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