Publication date: Available online 26 April 2018 Source:Discrete Applied Mathematics
Author(s): Carlile Lavor, Leo Liberti, Bruce Donald, Bradley Worley, Benjamin Bardiaux, Thérèse E. Malliavin, Michael Nilges
Nuclear Magnetic Resonance (NMR) experiments provide distances between nearby atoms of a protein molecule. The corresponding structure determination problem is to determine the 3D protein structure by exploiting such distances. We present a new order on the atoms of the protein, based on information from the chemistry of proteins and NMR experiments, which allows us to formulate the problem as a combinatorial search. Additionally, this order tells us what kind of NMR distance information is crucial to understand the cardinality of the solution set of the problem and its computational complexity.
[NMR paper] Polyproline is a minimal antifreeze protein mimetic and enhances the cryopreservation of cell monolayers
Polyproline is a minimal antifreeze protein mimetic and enhances the cryopreservation of cell monolayers
Tissue engineering, gene therapy, drug screening and emerging regenerative medicine therapies are fundamentally reliant on high-quality adherent cell culture, but current methods to cryopreserve cells in this format can give low cell yields and requires large volumes of solvent 'antifreezes'. Herein we report polyproline is a minimum (bio)synthetic mimic of antifreeze proteins, which is accessible by solution, solid phase and recombinant methods. We demonstrate that polyproline has...
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Impact of spin label rigidity on extent and accuracy of distance information from PRE data
Impact of spin label rigidity on extent and accuracy of distance information from PRE data
Abstract
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of...
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05-13-2017 02:08 PM
[NMR paper] The determination of pair distance distribution by double electron-electron resonance: Regularization by the length of distance discretization with Monte Carlo calculations
The determination of pair distance distribution by double electron-electron resonance: Regularization by the length of distance discretization with Monte Carlo calculations
Publication date: Available online 2 June 2016
Source:Journal of Magnetic Resonance</br>
Author(s): Sergei A. Dzuba</br>
Pulsed double electron-electron resonance technique (DEER, or PELDOR) is applied to study conformations and aggregation of peptides, proteins, nucleic acids, and other macromolecules. For a pair of spin labels, experimental data allows for determination of their distance...
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06-03-2016 04:52 PM
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
NMR, biophysical and biochemical studies reveal the minimal calmodulin-binding domain of the HIV-1 matrix protein.
J Biol Chem. 2011 Jul 28;
Authors: Samal AB, Ghanam RH, Fernandez TF, Monroe EB, Saad JS
Subcellular distribution of Calmodulin (CaM) in human immunodeficiency virus type-1 (HIV-1) infected cells is distinct from that observed in uninfected cells. CaM has been shown to interact and co-localize with the HIV-1 Gag protein...
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07-30-2011 11:23 AM
[NMR paper] Protein structure elucidation from minimal NMR data: the CLOUDS approach.
Protein structure elucidation from minimal NMR data: the CLOUDS approach.
Related Articles Protein structure elucidation from minimal NMR data: the CLOUDS approach.
Methods Enzymol. 2005;394:261-95
Authors: Grishaev A, Llinás M
In this chapter we review automated methods of protein NMR data analysis and expand on the assignment-independent CLOUDS approach. As presented, given a set of reliable NOEs it is feasible to derive a spatial H-atom distribution that provides a low-resolution image of the protein structure. In order to generate such a...
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11-24-2010 11:14 PM
[NMR paper] Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD
Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Related Articles Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Biochemistry. 2003 Dec 2;42(47):13856-68
Authors: Hu H, Clarkson MW, Hermans J, Lee AL
To gain physical insights into how proteins respond to changes in pH, the picosecond to nanosecond time scale dynamics of the small serine protease inhibitor eglin c have been studied by NMR spin relaxation experiments and MD simulations under two...
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11-24-2010 09:16 PM
[NMR paper] Automated protein fold determination using a minimal NMR constraint strategy.
Automated protein fold determination using a minimal NMR constraint strategy.
Related Articles Automated protein fold determination using a minimal NMR constraint strategy.
Protein Sci. 2003 Jun;12(6):1232-46
Authors: Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution...
Minimal NMR distance information for rigidity of protein graphs
Linear Mode
