Book ChapterDOI
Inferring and Using Protein Quaternary Structure Information from Crystallographic Data.
Sucharita Dey,Emmanuel D. Levy +1 more
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TLDR
Methods devised to discriminate between both types of contacts are reviewed and resources for downloading protein quaternary structure information and identifying high-confidence quaternARY structures are described.Abstract:
A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.read more
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Journal ArticleDOI
Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering
TL;DR: This work stresses the remarkable potential of symmetric homo‐oligomers to agglomerate even by single surface point mutations, and reviews the double‐edged nature of this potential: how aberrant assemblies resulting fromagglomeration can lead to disease, but also how agglomership can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
Journal ArticleDOI
Investigation of quaternary structure of aggregating 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans: In the pursuit of consensus of various biophysical techniques.
Kamila Sofińska,Agnieszka M. Wojtkiewicz,Patrycja Wójcik,Olga Zastawny,Maciej Guzik,Agnieszka Winiarska,Piotr Waligórski,Michał Cieśla,Jakub Barbasz,Maciej Szaleniec +9 more
TL;DR: The quaternary structure of FAD-dependent 3-ketosteroid dehydrogenase (AcmB) from Sterolibacterium denitrificans, the protein that in solution forms massive aggregates is analyzed to observe that aggregation is most probably initiated by hydrophobic forces and then assisted by electrostatic attraction between negatively charged aggregates and positively charged monomers.
Journal ArticleDOI
PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry.
Sucharita Dey,Emmanuel D. Levy +1 more
TL;DR: In this article, the authors employ quaternary structure conservation across homologs to infer the biological relevance of hetero-oligomers, and compare the structures and compositions of heteroglobic complexes.
Journal ArticleDOI
A unified statistical potential reveals that amino acid stickiness governs nonspecific recruitment of client proteins into condensates
TL;DR: The stickiness of client proteins is sufficient to explain their differential partitioning within these two phase‐separated systems without taking into account the composition of the condensate, which implies that selective trafficking of Client proteins to distinct membraneless organelles requires recognition elements beyond the client sequence composition.
Posted ContentDOI
Desolvation Energy Explains Partitioning of Client Proteins into Condensates
TL;DR: In this article, a set of knowledge-based potentials were developed for the direct comparison between desolvation energy and pairwise interaction energy terms, and used these to examine experimental data from two phase-separated systems: protein cargo and client proteins dissolving within phase separated droplets made from FG repeat proteins of the nuclear pore complex.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Overview of the CCP4 suite and current developments.
Martyn Winn,Charles Ballard,Kevin Cowtan,Eleanor J. Dodson,Paul Emsley,Phil Evans,Ronan M. Keegan,Eugene Krissinel,Andrew G. W. Leslie,Airlie J. McCoy,Stuart McNicholas,Garib N. Murshudov,Navraj S. Pannu,E. Potterton,Harold R. Powell,Randy J. Read,Alexei A. Vagin,Keith S. Wilson +17 more
TL;DR: An overview of the CCP4 software suite for macromolecular crystallography is given.
Journal ArticleDOI
Inference of macromolecular assemblies from crystalline state.
E. Krissinel,Kim Henrick +1 more
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.
Journal ArticleDOI
On the Nature of Allosteric Transitions: A Plausible Model
TL;DR: "It is certain that all bodies whatsoever, though they have no sense, yet they have perception, and whether the body be alterant or alterec, evermore a perception precedeth operation; for else all bodies would be like one to another."
Journal ArticleDOI
The interpretation of protein structures: estimation of static accessibility.
B. Lee,Frederic M. Richards +1 more
TL;DR: The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.
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