2,472 research outputs found
Site-specific perturbations of alpha-synuclein fibril structure by the Parkinson's disease associated mutations A53T and E46K.
PMCID: PMC3591419This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Parkinson's disease (PD) is pathologically characterized by the presence of Lewy bodies (LBs) in dopaminergic neurons of the substantia nigra. These intracellular inclusions are largely composed of misfolded α-synuclein (AS), a neuronal protein that is abundant in the vertebrate brain. Point mutations in AS are associated with rare, early-onset forms of PD, although aggregation of the wild-type (WT) protein is observed in the more common sporadic forms of the disease. Here, we employed multidimensional solid-state NMR experiments to assess A53T and E46K mutant fibrils, in comparison to our recent description of WT AS fibrils. We made de novo chemical shift assignments for the mutants, and used these chemical shifts to empirically determine secondary structures. We observe significant perturbations in secondary structure throughout the fibril core for the E46K fibril, while the A53T fibril exhibits more localized perturbations near the mutation site. Overall, these results demonstrate that the secondary structure of A53T has some small differences from the WT and the secondary structure of E46K has significant differences, which may alter the overall structural arrangement of the fibrils
GeNMR: a web server for rapid NMR-based protein structure determination
GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15–25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca
Sparse random matrices and vibrational spectra of amorphous solids
A random matrix approach is used to analyze the vibrational properties of
amorphous solids. We investigated a dynamical matrix M=AA^T with non-negative
eigenvalues. The matrix A is an arbitrary real NxN sparse random matrix with n
independent non-zero elements in each row. The average values =0 and
dispersion =V^2 for all non-zero elements. The density of vibrational
states g(w) of the matrix M for N,n >> 1 is given by the Wigner quarter circle
law with radius independent of N. We argue that for n^2 << N this model can be
used to describe the interaction of atoms in amorphous solids. The level
statistics of matrix M is well described by the Wigner surmise and corresponds
to repulsion of eigenfrequencies. The participation ratio for the major part of
vibrational modes in three dimensional system is about 0.2 - 0.3 and
independent of N. Together with term repulsion it indicates clearly to the
delocalization of vibrational excitations. We show that these vibrations spread
in space by means of diffusion. In this respect they are similar to diffusons
introduced by Allen, Feldman, et al., Phil. Mag. B 79, 1715 (1999) in amorphous
silicon. Our results are in a qualitative and sometimes in a quantitative
agreement with molecular dynamic simulations of real and model glasses.Comment: 24 pages, 7 figure
Density of states in random lattices with translational invariance
We propose a random matrix approach to describe vibrational excitations in
disordered systems. The dynamical matrix M is taken in the form M=AA^T where A
is some real (not generally symmetric) random matrix. It guaranties that M is a
positive definite matrix which is necessary for mechanical stability of the
system. We built matrix A on a simple cubic lattice with translational
invariance and interaction between nearest neighbors. We found that for certain
type of disorder phonons cannot propagate through the lattice and the density
of states g(w) is a constant at small w. The reason is a breakdown of affine
assumptions and inapplicability of the elasticity theory. Young modulus goes to
zero in the thermodynamic limit. It strongly reminds of the properties of a
granular matter at the jamming transition point. Most of the vibrations are
delocalized and similar to diffusons introduced by Allen, Feldman et al., Phil.
Mag. B v.79, 1715 (1999).Comment: 4 pages, 5 figure
NMR Derived Model of GTPase Effector Domain (GED) Self Association: Relevance to Dynamin Assembly
Self-association of dynamin to form spiral structures around lipidic vesicles during endocytosis is largely mediated by its ‘coiled coil’ GTPase Effector Domain (GED), which, in vitro, self-associates into huge helical assemblies. Residue-level structural characterizations of these assemblies and understanding the process of association have remained a challenge. It is also impossible to get folded monomers in the solution phase. In this context, we have developed here a strategy to probe the self-association of GED by first dissociating the assembly using Dimethyl Sulfoxide (DMSO) and then systematically monitoring the refolding into helix and concomitant re-association using NMR spectroscopy, as DMSO concentration is progressively reduced. The short segment, Arg109 - Met116, acts as the nucleation site for helix formation and self-association. Hydrophobic and complementary charge interactions on the surfaces drive self-association, as the helices elongate in both the directions resulting in an antiparallel stack. A small N-terminal segment remains floppy in the assembly. Following these and other published results on inter-domain interactions, we have proposed a plausible mode of dynamin self assembly
Backbone and side-chain 1H, 15N and 13C resonance assignments of S18Y mutant of ubiquitin carboxy-terminal hydrolase L1
Ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), also known as PGP9.5, is a protein of 223 amino acids. Although it was originally characterized as a deubiquitinating enzyme, recent studies indicate that it also functions as a ubiquitin (Ub) ligase and a mono-Ub stabilizer. It is highly abundant in brain, constituting up to 2% of total brain proteins. Down-regulation and extensive oxidative modification of UCH-L1 have been observed in the brains of Alzheimer’s disease (AD) and Parkinson’s disease (PD) patients. Mutations in the UCH-L1 gene have been reported to be linked to Parkinson’s disease, in particular, the I93 M variant is associated with a higher susceptibility of PD in contrast to a higher protection against PD for the S18Y variant. Hence, the structure of UCH-L1 and the underlying effects of disease associated mutations on the structure and function of UCH-L1 are of considerable interest. Here, we report the NMR spectral assignments of the S18Y human UCH-L1 mutant with the aim to obtain better understanding about the risk of Parkinson’s disease against structural and dynamical changes induced by this mutation on UCH-L1
BioMagResBank
The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pKa values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional 1H and 13C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions
Large Deviations of the Maximum Eigenvalue in Wishart Random Matrices
We compute analytically the probability of large fluctuations to the left of
the mean of the largest eigenvalue in the Wishart (Laguerre) ensemble of
positive definite random matrices. We show that the probability that all the
eigenvalues of a (N x N) Wishart matrix W=X^T X (where X is a rectangular M x N
matrix with independent Gaussian entries) are smaller than the mean value
=N/c decreases for large N as , where \beta=1,2 correspond respectively to
real and complex Wishart matrices, c=N/M < 1 and \Phi_{-}(x;c) is a large
deviation function that we compute explicitly. The result for the Anti-Wishart
case (M < N) simply follows by exchanging M and N. We also analytically
determine the average spectral density of an ensemble of constrained Wishart
matrices whose eigenvalues are forced to be smaller than a fixed barrier. The
numerical simulations are in excellent agreement with the analytical
predictions.Comment: Published version. References and appendix adde
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