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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Protocols for Efficient Simulations of Long-Time Protein Dynamics Using Coarse-Grained CABS Model
Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long-time scale protein folding events at reasonable computational cost. Depending on the design of a CG model, the simulation protocols vary from highly case-specific—requiring user-defined assumptions about the folding scenario—to more sophisticated blind prediction methods for which only a protein sequence is required. Here we describe the framework protocol for the simulations of long-term dynamics of globular proteins, with the use of the CABS CG protein model and sequence data. The simulations can start from a...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite
Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein–protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein structures, which are either experimentally solved or computationally modeled, and outputs a series of probable complex structures. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes
In protein docking we aim to find the structure of the complex formed when two proteins interact. Protein–protein interactions are crucial for cell function. Here we discuss the usage of DOCK/PIERR. In DOCK/PIERR, a uniformly discrete sampling of orientations of one protein with respect to the other, are scored, followed by clustering, refinement, and reranking of structures. The novelty of this method lies in the scoring functions used. These are obtained by examining hundreds of millions of correctly and incorrectly docked structures, using an algorithm based on mathematical programming, with provable convergence p...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Predicting the Structure of Protein–Protein Complexes Using the SwarmDock Web Server
Protein–protein interactions drive many of the biological functions of the cell. Any two proteins have the potential to interact; however, whether the interactions are of biological significance is dependent on a number of complicated factors. Thus, modelling the three-dimensional structure of protein–protein complexes is still considered to be a complex endeavor. Nevertheless, many experimentalists now wish to boost their knowledge of protein–protein interactions, well beyond complexes resolved experimentally, and for them to be able to do so it is important they are able to effectively and confidently p...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Complexes with HADDOCK”
Protein–protein interactions lie at the heart of most cellular processes. Determining their high-resolution structures by experimental methods is a nontrivial task, which is why complementary computational approaches have been developed over the years. To gain structural and dynamical insight on an atomic scale in these interactions, computational modeling must often be complemented by low-resolution experimental information. For this purpose, we developed the user-friendly HADDOCK webserver, the interface to our biomolecular docking program, which can make use of a variety of low-resolution data to drive the docking...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Prediction of Intrinsic Disorder in Proteins Using MFDp2
Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant across all kingdoms of life, particularly in eukaryotes, and are implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel webserver for accurate sequence-based prediction of protein disorder which also outputs well-described sequence-derived information that allows profiling the p...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
POODLE: Tools Predicting Intrinsically Disordered Regions of Amino Acid Sequence
Protein intrinsic disorder, a widespread phenomenon characterized by a lack of stable three-dimensional structure, is thought to play an important role in protein function. In the last decade, dozens of computational methods for predicting intrinsic disorder from amino acid sequences have been developed. They are widely used by structural biologists not only for analyzing the biological function of intrinsic disorder but also for finding flexible regions that possibly hinder successful crystallization of the full-length protein. In this chapter, I introduce Prediction Of Order and Disorder by machine LEarning (POODLE), whi...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Geometric Simulation of Flexible Motion in Proteins
This chapter describes the use of physically simplified analysis and simulation methods—pebble-game rigidity analysis, coarse-grained elastic network modeling, and template-based geometric simulation—to explore flexible motion in protein structures. Substantial amplitudes of flexible motion can be explored rapidly in an all-atom model, retaining realistic covalent bonding, steric exclusion, and a user-defined network of noncovalent polar and hydrophobic interactions, using desktop computing resources. Detailed instructions are given for simulations using FIRST/FRODA software installed on a UNIX/Linux workstatio...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Carbon–Deuterium Bonds as Non-perturbative Infrared Probes of Protein Dynamics, Electrostatics, Heterogeneity, and Folding
Vibrational spectroscopy is uniquely able to characterize protein dynamics and microenvironmental heterogeneity because it possesses an inherently high temporal resolution and employs probes of ultimately high structural resolution—the bonds themselves. The use of carbon–deuterium (C–D) bonds as vibrational labels circumvents the spectral congestion that otherwise precludes the use of vibrational spectroscopy to proteins and makes the observation of single vibrations within a protein possible while being wholly non-perturbative. Thus, C–D probes can be used to site-specifically characterize conforma...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Probing Backbone Dynamics with Hydrogen/Deuterium Exchange Mass Spectrometry
Protein dynamics can be probed by the solution technique amide hydrogen/deuterium exchange. The exchange rate of hydrogen for deuterium along a peptide backbone is dependent on the extent of hydrogen bonding from secondary structure, accessibility by D2O, and protein motions. Both global and local conformational changes that alter bonding or structure will lead to changes in the amount of deuterium incorporated. The deuterium can be localized via pepsin digestion of the protein and quantified by electrospray ionization mass spectrometry through the mass shifts of the resulting peptides. The technique is emerging as an esse...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Protein Structural Dynamics Revealed by Site-Directed Spin Labeling and Multifrequency EPR
Multifrequency electron paramagnetic resonance (EPR) of spin-labeled protein is a powerful spectroscopic technique to study protein dynamics on the rotational correlation time scale from 100 ps to 100 ns. Nitroxide spin probe, attached to cysteine residue, reports on local topology within the labeling site, dynamics of protein domains reorientation, and protein global tumbling in solution. Due to spin probe’s magnetic tensors anisotropy, its mobility is directly reflected by the EPR lineshape. The multifrequency approach significantly decreases ambiguity of EPR spectra interpretation. The approach, described in this ...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Confocal Single-Molecule FRET for Protein Conformational Dynamics
Single-molecule Fӧrster-type resonance energy transfer (smFRET) is a unique technique capable of following conformational motions of individual protein molecules. The direct observation of individual proteins provides rich information that would be washed away in ensemble measurements, hence opening up new avenues for establishing the protein structure-function relationships through dynamics. Retrieving dynamics information of biomolecular motions via smFRET, though, requires careful experiment design and rigorous treatment of single-molecule statistics. Here, we describe the rudimentary steps for an smFRET experimen...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
CPMG Relaxation Dispersion
NMR relaxation is sensitive to molecular and internal motion of proteins. 15N longitudinal relaxation rate (R
1), transverse relaxation rate (R
2), and {1H}-15N Nuclear Overhauser Effect (NOE) experiments are often performed to globally elucidate protein dynamics, primarily on the sub-nanosecond timescale. In contrast, constant relaxation time R
2 dispersion experiments are applied to characterize protein equilibrium conformations that interconvert on the millisecond timescale. Information on local conformational equilibria of proteins provides important insights about protei...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Monitoring Side-Chain Dynamics of Proteins Using 2H Relaxation
Nuclear magnetic resonance (NMR) is a powerful technique capable of monitoring a wide range of motions in proteins on a per residue basis. A variety of 2H relaxation experiments have been developed for monitoring side-chain methyl group motions on the picosecond–nanosecond timescale. These experiments enable determination of the order parameter, S
2
axis, which reports on the rigidity of the C-CH3 bond for side-chain methyl groups. The application of a commonly used subset of these experiments is described in this chapter. It is intended to serve as a practical guide to investigators i...
Source: Springer protocols feed by Protein Science - September 27, 2013 Category: Biochemistry Source Type: news
Imaging the Activity of Ras Superfamily GTPase Proteins in Small Subcellular Compartments in Neurons
Resolving the spatiotemporal dynamics of intracellular signaling is important for understanding the molecular mechanisms of various cellular processes induced by extracellular signals. Two-photon fluorescence lifetime imaging microscopy (2pFLIM) in combination with a fluorescence resonance energy transfer (FRET)-based signaling sensors allows one to image signaling within small subcellular compartments, such as dendritic spines of neurons, with high sensitivity and spatiotemporal resolution. In this protocol, we describe the procedures and equipment required for imaging intracellular signaling activity, with a particular f...
Source: Springer protocols feed by Protein Science - September 22, 2013 Category: Biochemistry Source Type: news
