Literature DB >> 14675549

Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?

Alice Vrielink1, Nicole Sampson.   

Abstract

Recent technical advances in crystallographic analysis, particularly highly focused and high brilliance synchrotron beam lines, have significantly improved the resolutions that are attainable for many macromolecular crystal structures. The Protein Data Bank (http://www.rcsb.org/pdb/) contains an increasing number of atomic resolution structures, which are providing a wealth of structural information that was not previously visible in lower resolution electron density maps. Here, we review the importance of visualizing hydrogen atoms and multiple sidechain conformations or anisotropy, as well as substrate strain, at sub-Angstrom resolution. The additional structural features that are visible in the electron density maps as a result of atomic resolution data provide a better understanding of the catalytic mechanisms of cholesterol oxidase, ribonuclease A, beta-lactamase, serine proteases, triosephosphate isomerase and endoglucanase.

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Year:  2003        PMID: 14675549     DOI: 10.1016/j.sbi.2003.10.012

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  13 in total

1.  Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.

Authors:  Paul A Sigala; Daniel A Kraut; Jose M M Caaveiro; Brandon Pybus; Eliza A Ruben; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2008-09-23       Impact factor: 15.419

2.  Modeling multiple species of nicotine and deschloroepibatidine interacting with alpha4beta2 nicotinic acetylcholine receptor: from microscopic binding to phenomenological binding affinity.

Authors:  Xiaoqin Huang; Fang Zheng; Peter A Crooks; Linda P Dwoskin; Chang-Guo Zhan
Journal:  J Am Chem Soc       Date:  2005-10-19       Impact factor: 15.419

Review 3.  The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals.

Authors:  Sajesh P Thomas; Amol G Dikundwar; Sounak Sarkar; Mysore S Pavan; Rumpa Pal; Venkatesha R Hathwar; Tayur N Guru Row
Journal:  Molecules       Date:  2022-06-08       Impact factor: 4.927

4.  The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.

Authors:  Galen J Correy; Daniel W Kneller; Gwyndalyn Phillips; Swati Pant; Silvia Russi; Aina E Cohen; George Meigs; James M Holton; Stefan Gahbauer; Michael C Thompson; Alan Ashworth; Leighton Coates; Andrey Kovalevsky; Flora Meilleur; James S Fraser
Journal:  Sci Adv       Date:  2022-05-27       Impact factor: 14.957

5.  Structure of Alzheimer's disease amyloid precursor protein copper-binding domain at atomic resolution.

Authors:  Geoffrey Kwai-Wai Kong; Julian J Adams; Roberto Cappai; Michael W Parker
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-09-19

6.  The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.

Authors:  Weixiao Yuan Wahlgren; Gábor Pál; József Kardos; Pálma Porrogi; Borbála Szenthe; András Patthy; László Gráf; Gergely Katona
Journal:  J Biol Chem       Date:  2010-11-21       Impact factor: 5.157

7.  Towards automated crystallographic structure refinement with phenix.refine.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Nathaniel Echols; Jeffrey J Headd; Nigel W Moriarty; Marat Mustyakimov; Thomas C Terwilliger; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-03-16

8.  High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

Authors:  Akifumi Higashiura; Kazunori Ohta; Mika Masaki; Masaru Sato; Koji Inaka; Hiroaki Tanaka; Atsushi Nakagawa
Journal:  J Synchrotron Radiat       Date:  2013-10-05       Impact factor: 2.616

9.  On macromolecular refinement at subatomic resolution with interatomic scatterers.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Paul D Adams; Vladimir Y Lunin; Alexandre Urzhumtsev
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-10-17

Review 10.  Contributions of charge-density research to medicinal chemistry.

Authors:  Birger Dittrich; Chérif F Matta
Journal:  IUCrJ       Date:  2014-09-23       Impact factor: 4.769

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