Publication date: Available online 7 August 2014 Source:Structure
Author(s): Nikolaos*G. Sgourakis , Kannan Natarajan , Jinfa Ying , Beat Vogeli , Lisa*F. Boyd , David*H. Margulies , Ad Bax
Immunoevasins are key proteins used by viruses to subvert host immune responses. Determining their high-resolution structures is key to understanding virus-host interactions toward the design of vaccines and other antiviral therapies. Mouse cytomegalovirus encodes a unique set of immunoevasins, the m02-m06 family, that modulates major histocompatibility complex class I (MHC-I) antigen presentation to CD8+ T*cells and natural killer cells. Notwithstanding the large number of genetic and functional studies, the structural biology of immunoevasins remains incompletely understood, largely because of crystallization bottlenecks. Here we implement a*technology using sparse nuclear magnetic resonance data and integrative Rosetta modeling to determine the structure of the m04/gp34 immunoevasin extracellular domain. The structure reveals a ? fold that is representative of the m02-m06 family of viral proteins, several of which are known to bind MHC-I molecules and interfere with antigen presentation, suggesting its role as a diversified immune regulation module. Graphical abstract
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Sgourakis et*al. describe a hybrid approach for determining the structure of proteins using sparse NMR datasets coupled with molecular modeling. Using this new approach, the structure of a viral protein has been determined to high precision, a first step in understanding the molecular basis of its function.
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology]
Protein structure modeling using sparse NMR data
Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D....
Date: 2012-06-19
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...
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06-20-2012 02:28 AM
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set.
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set.
Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set.
J Mol Biol. 2011 May 23;
Authors: Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A
The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein ?-barrel assembly machine in E. coli. The...
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06-01-2011 02:30 PM
Herpes 3D: NMR reveals viral protein hijacking
Herpes 3D: NMR reveals viral protein hijacking
UK scientists have used NMR for the first time to develop a 3D picture of a herpes virus protein interacting with a key part of the human cellular machinery. The study improves our understanding of how the virus hijacks human cells and could eventually lead to new targets for drug therapy.
Source: Spectroscopynow.com
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01-15-2011 02:09 AM
[NMR paper] TOUCHSTONEX: protein structure prediction with sparse NMR data.
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Proteins. 2003 Nov 1;53(2):290-306
Authors: Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J
TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly...
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[NMR paper] De novo protein structure determination using sparse NMR data.
De novo protein structure determination using sparse NMR data.
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J Biomol NMR. 2000 Dec;18(4):311-8
Authors: Bowers PM, Strauss CE, Baker D
We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...
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[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se
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http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets.
J Mol Biol. 1999 Jan 29;285(4):1691-710
Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE
We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...
The Structure of Mouse Cytomegalovirus m04 Protein Obtained from Sparse NMR Data Reveals a Conserved Fold of the m02-m06 Viral Immune Modulator Family
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