We introduce AlphaFold-NMR, a novel approach to NMR structure determination that reveals previously undetected protein conformational states. Unlike conventional NMR methods which rely on NOE-derived spatial restraints, AlphaFold-NMR combines AI-driven conformational sampling with Bayesian scoring of realistic protein models against NOESY and chemical shift data. This method uncovers alternative conformational states of the enzyme Gaussia luciferase, involving large-scale changes in the lid,...
[NMR paper] Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data
Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data
Protein-polypeptide interactions, including those involving intrinsically-disordered peptides and intrinsically-disordered regions of protein binding partners, are crucial for many biological functions. However, experimental structure determination of protein-peptide complexes can be challenging. Computational methods, while promising, generally require experimental data for validation and refinement. Here we present CSP_Rank, an integrated modeling...
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[NMR paper] Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR
Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR
Recent advances in molecular modeling using deep learning can revolutionize our understanding of dynamic protein structures. NMR is particularly well-suited for determining dynamic features of biomolecular structures. The conventional process for determining biomolecular structures from experimental NMR data involves its representation as conformation-dependent restraints, followed by generation of structural models guided by these spatial restraints. Here we describe an alternative approach:...
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Hidden Structural Codes in Protein Intrinsic Disorder
Hidden Structural Codes in Protein Intrinsic Disorder
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00721/20171006/images/medium/bi-2017-00721n_0006.gif
Biochemistry
DOI: 10.1021/acs.biochem.7b00721
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[NMR paper] Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques.
Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques.
Related Articles Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques.
J Biomol Struct Dyn. 2015 Jan 14;:1-18
Authors: Naiyer A, Hassan MI, Islam A, Sundd M, Ahmad F
Abstract
Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at...
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Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion.
Proc Natl Acad Sci U S A. 2011 May 11;
Authors: Meinhold DW, Wright PE
Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use (15)N, , and (13)CO NMR R(2)...
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[NMR paper] Structural analysis of non-native states of proteins by NMR methods.
Structural analysis of non-native states of proteins by NMR methods.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structural analysis of non-native states of proteins by NMR methods.
Curr Opin Struct Biol. 1996 Feb;6(1):24-30
Authors: Shortle DR
Established NMR methods are increasingly being applied to the non-native states of proteins. For small denatured proteins, full assignment of proton, 15N and 13C resonances is often straightforward. Sensitive methods exist...
Hidden structural states of proteins revealed by conformer selection with AlphaFold-NMR
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