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From protein structure to function via single crystal optical spectroscopy

The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radi...

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Autores principales: Ronda, Luca, Bruno, Stefano, Bettati, Stefano, Storici, Paola, Mozzarelli, Andrea
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428442/
https://www.ncbi.nlm.nih.gov/pubmed/25988179
http://dx.doi.org/10.3389/fmolb.2015.00012
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author Ronda, Luca
Bruno, Stefano
Bettati, Stefano
Storici, Paola
Mozzarelli, Andrea
author_facet Ronda, Luca
Bruno, Stefano
Bettati, Stefano
Storici, Paola
Mozzarelli, Andrea
author_sort Ronda, Luca
collection PubMed
description The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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spelling pubmed-44284422015-05-18 From protein structure to function via single crystal optical spectroscopy Ronda, Luca Bruno, Stefano Bettati, Stefano Storici, Paola Mozzarelli, Andrea Front Mol Biosci Molecular Biosciences The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. Frontiers Media S.A. 2015-04-28 /pmc/articles/PMC4428442/ /pubmed/25988179 http://dx.doi.org/10.3389/fmolb.2015.00012 Text en Copyright © 2015 Ronda, Bruno, Bettati, Storici and Mozzarelli. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Ronda, Luca
Bruno, Stefano
Bettati, Stefano
Storici, Paola
Mozzarelli, Andrea
From protein structure to function via single crystal optical spectroscopy
title From protein structure to function via single crystal optical spectroscopy
title_full From protein structure to function via single crystal optical spectroscopy
title_fullStr From protein structure to function via single crystal optical spectroscopy
title_full_unstemmed From protein structure to function via single crystal optical spectroscopy
title_short From protein structure to function via single crystal optical spectroscopy
title_sort from protein structure to function via single crystal optical spectroscopy
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428442/
https://www.ncbi.nlm.nih.gov/pubmed/25988179
http://dx.doi.org/10.3389/fmolb.2015.00012
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