Related ArticlesConstructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.
J Chem Phys. 2015 Dec 28;143(24):243141
Authors: Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN
Abstract
The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein's functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.
Analyzing protein structures in their native environment - MIT News
Analyzing protein structures in their native environment - MIT News
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Analyzing protein structures in their native environment
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Until now, it has been difficult to fully characterize the different structures that proteins can take on in their natural environments. However, using a new technique known as sensitivity-enhanced nuclear magnetic resonance (NMR), MIT researchers have ...
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11-22-2015 01:36 AM
Analyzing Protein Structures in Their Native Environment - Bioscience Technology
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Analyzing Protein Structures in Their Native Environment
Bioscience Technology
However, using a new technique known as sensitivity-enhanced nuclear magnetic resonance (NMR), MIT researchers have shown that they can analyze the structure that a yeast protein forms as it interacts with other proteins in a cell. Using this type of ...
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Analyzing Protein Structures in Their Native...
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10-13-2015 05:51 AM
Analyzing protein structures in their native environment - R & D Magazine
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Analyzing protein structures in their native environment
R & D Magazine
However, using a new technique known as sensitivity-enhanced nuclear magnetic resonance (NMR), Massachusetts Institute of Technology (MIT) researchers have shown that they can analyze the structure that a yeast protein forms as it interacts with other ...
Analyzing protein structures in their native environment - R & D Magazine
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10-12-2015 01:41 PM
Analyzing protein structures in their native environment - ScienceBlog.com (blog)
Analyzing protein structures in their native environment - ScienceBlog.com (blog)
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Analyzing protein structures in their native environment
ScienceBlog.com (blog)
Until now, it has been difficult to fully characterize the different structures that proteins can take on in their natural environments. However, using a new technique known as sensitivity-enhanced nuclear magnetic resonance (NMR), MIT...
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10-09-2015 03:05 AM
[NMR paper] 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate.
19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate.
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Biochemistry. 2013 Aug 1;
Authors: Kitevski-Leblanc JL, Hoang J, Thach W, Larda ST, Prosser RS
Abstract
While many proteins are recognized to undergo folding via an intermediate, the microscopic nature of folding intermediates is less understood. In this study, 19F NMR and near UV circular dichroism (CD) are used to characterize a transition to a thermal folding intermediate of calmodulin, a...
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08-04-2013 03:18 AM
[NMR paper] Solid State NMR Strategy for Characterizing Native Membrane Protein Structures.
Solid State NMR Strategy for Characterizing Native Membrane Protein Structures.
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Acc Chem Res. 2013 Mar 7;
Authors: Murray DT, Das N, Cross TA
Abstract
Unlike water soluble proteins, the structures of helicaltransmembrane proteins depend on a very complex environment. These proteins sit in the midst of dramatic electrical and chemical gradients and are often subject to variations in the lateral pressure profile, order parameters, dielectric...
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03-09-2013 11:05 AM
[NMR paper] Generation of native-like protein structures from limited NMR data, modern force fiel
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
Related Articles Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
J Biomol NMR. 2005 Jan;31(1):59-64
Authors: Chen J, Won HS, Im W, Dyson HJ, Brooks CL
Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality...
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11-24-2010 11:14 PM
[NMR paper] Folding Trp-cage to NMR resolution native structure using a coarse-grained protein mo
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
Related Articles Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.
Biophys J. 2005 Jan;88(1):147-55
Authors: Ding F, Buldyrev SV, Dokholyan NV
We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability...
Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.
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