Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field.

Becky L Eggimann, Vitaly V Vostrikov, Gianluigi Veglia, J Ilja Siepmann

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Article in Theoretical chemistry accounts, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package.BMC bioinformatics · 2020
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5 · Who and what money

Authors and funding

4 authors.

Becky L EggimannDepartment of Chemistry, Chemical Theory Center, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA.

Vitaly V VostrikovMolecular Biology and Biophysics, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.

Gianluigi VegliaDepartment of Chemistry, Chemical Theory Center, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA.

J Ilja SiepmannDepartment of Chemistry, Chemical Theory Center, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA.

Funding

NMR Structural Analysis of Calcium Regulation in MuscleR01GM064742 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI VEGLIA, GIANLUIGI · 2002 to 2019

$7.1M

Structural Basis Of Dilated CardiomyopathyR01GM072701 · NIGMS · UNIVERSITY OF MINNESOTA · PI VEGLIA, GIANLUIGI · 2007 to 2015

$2.4M

NIGMS NIH HHS R01 GM064742NIGMS NIH HHS R01 GM072701

6 · The paper itself

Abstract

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy.

Indexed as

Dipolar wavesHelical proteinsNMRParamagnetic relaxation enhancementsResidual dipolar couplingsSimulated annealingStructural determination

Identifiers

PMID24639619

DOI10.1007/s00214-013-1388-y

PMCPMC3951508

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