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ARTICLES Determining the architectures of macromolecular assemblies

by Frank Alber , Svetlana Dokudovskaya , Liesbeth M Veenhoff , Wenzhu Zhang , Julia Kipper , { , Damien Devos , { , Adisetyantari Suprapto , { , Orit Karni-Schmidt , { , Rosemary Williams , Brian T Chait , Michael P Rout , Andrej Sali
"... To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into ..."
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To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data

Accurate Structural Correlations from Maximum Likelihood Superpositions

by Douglas L. Theobald, Deborah S. Wuttke
"... The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biom ..."
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biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related

Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins. PLoS One 2012

by Elio A. Cino, Mikko Karttunen, Wing-yiu Choy
"... Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by ..."
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are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three

All-atom contacts: a new approach to structure validation

by Jane S Richardson - Methods Biochem. Anal , 2003
"... The enormous wealth of macromolecular structure data already available and the even greater wealth soon to come—from structural genomics, from the push for atomic-resolution structures, and from the push to solve much larger biological complexes —provide a treasure trove of functional, interactional ..."
Abstract - Cited by 2 (1 self) - Add to MetaCart
are indicated by a high crystallographic B-factor or highly divergent conformations in an NMR ensemble. If a particular part of a structure is important to the question being asked, such telltale signs should always be heeded.

Author's personal copy Linking folding and binding This review comes from a themed issue on Folding and Binding Edited

by Peter E Wright , Jane Dyson , Alan Fersht , Valerie Daggett , 2009
"... Many cellular proteins are intrinsically disordered and undergo folding, in whole or in part, upon binding to their physiological targets. The past few years have seen an exponential increase in papers describing characterization of intrinsically disordered proteins, both free and bound to targets. ..."
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. Although NMR spectroscopy remains the favored tool, a number of new biophysical techniques are proving exceptionally useful in defining the limits of the conformational ensembles. Advances have been made in prediction of the recognition elements in disordered proteins, in elucidating the kinetics
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