Publication date: 7 June 2016 Source:Biophysical Journal, Volume 110, Issue 11
Author(s): Maher*M. Kassem, Yong Wang, Wouter Boomsma, Kresten Lindorff-Larsen
Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular ?-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology*and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means.
[NMR paper] NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
Related Articles NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
PLoS One. 2013;8(12):e83532
Authors: Mao W, Cong P, Wang Z, Lu L, Zhu Z, Li T
Abstract
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are...
nmrlearner
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01-01-2014 03:05 PM
CS23D - generating protein structure from NMR chemical shifts and sequence homology
CS23D website
CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. CS23D uses a combination of maximal subfragment assembly, chemical shift threading, shift-based torsion angle prediction and chemical shift refinement to generate and refine the protein coordinates. CS23D accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein normally within 10-15 minutes (3 hours max). CS23D performance is dependent on the completeness of the chemical shift assignments and...
markber
NMR software
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02-23-2012 09:40 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts.
Related Articles Sequence-dependent correction of random coil NMR chemical shifts.
J Am Chem Soc. 2001 Apr 4;123(13):2970-8
Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ
Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
nmrlearner
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11-19-2010 08:32 PM
[NMR paper] The impact of direct refinement against proton chemical shifts on protein structure d
The impact of direct refinement against proton chemical shifts on protein structure determination by NMR.
Related Articles The impact of direct refinement against proton chemical shifts on protein structure determination by NMR.
J Magn Reson B. 1995 Jun;107(3):293-7
Authors: Kuszewski J, Gronenborn AM, Clore GM
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08-22-2010 03:41 AM
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
Abstract We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and 13Cβ chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-13Cγ, Promega calculates the statistical probability that a Xaa-Pro peptide bond...
Analysis of NMR Chemical Shifts in Peptide & Protein Structure Determination-Wang '08
Analysis of NMR Chemical Shifts in Peptide and Protein Structure Determination
By Liya Wang (2008)
Amazon book description
Chemical shifts provide detailed information about non-covalent structure, solvent interactions, ionization constants, ring orientations, hydrogen bond interactions, and other phenomena. Since different chemical shift data sets are not necessarily comparable without corrections or adjustments, the applicability of statistical analysis of NMR chemical shifts to biomolecules has so far been limited. We use the term "congruent" to describe data sets that can be...
Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation
Linear Mode
