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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.Density Functional Theory–Broken Symmetry (DFT–BS) Methodology Applied to Electronic and Magnetic Properties of Bioinorganic Prosthetic Groups
The goal of this “how to” chapter is to present in a way as simple and practical as possible some of the concepts, key issues, and practices behind the so-called broken symmetry (BS) state which is widely used within the density functional theory (DFT) (for a very nice but thoughtful introduction to DFT (without equations!), read Perdew et al. (J Chem Theory Comput 5:902–908, 2009)) community to compute energetic as well as spectroscopic properties pertaining to (poly-)radicals, bioinorganic clusters (especially those containing transition metal ions), etc. Such properties encompass exchange coupling cons...
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
Quantum Mechanical Methods for the Investigation of Metalloproteins and Related Bioinorganic Compounds
It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H2, O2, and N2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure–activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very ...
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
X-Ray Crystallographic Studies of Metalloproteins
Many proteins require metals for their physiological function. In combination with spectroscopic characterizations, X-ray crystallography is a very powerful method to correlate the function of protein-bound metal sites with their structure. Due to their special X-ray scattering properties, specific metals may be located in metalloprotein structures and eventually used for phasing the diffracted X-rays by the method of Multi-wavelength Anomalous Dispersion (MAD). How this is done is the principle subject of this chapter. Attention is also given to the crystallographic characterization of different oxidation states of redox ...
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
X-Ray Absorption Spectroscopy of Metalloproteins
Metalloproteins are enormously important in biology. While a variety of techniques exist for studying metals in biology, X-ray absorption spectroscopy is particularly useful in that it can determine the local electronic and physical structure around the metal center, and is one of the few avenues for studying “spectroscopically silent” metal ions like Zn(II) and Cu(I) that have completely filled valence bands. While X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) are useful for studying metalloprotein structure, they suffer the limitation that the detected signa...
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
Mössbauer Spectroscopy
Given its ability to detect all iron centers, to identify their electronic structures, and to quantify the ratios of the different iron forms present in a sample, many researchers turn to Mössbauer spectroscopy when wanting to address structural and mechanistic questions involving iron proteins. Yet, this technique applied to biochemistry is provided by only a few dedicated teams in the world. Technical difficulties ranging from sample preparation to data analysis and interpretation make necessary the collaboration between biochemists and Mössbauer spectroscopists. This chapter will be confined to iron Mössb...
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
Study of Metalloproteins Using Continuous Wave Electron Paramagnetic Resonance (EPR)
Electron paramagnetic resonance (EPR) is an invaluable tool when studying systems with paramagnetic centers. It is a sensitive spectroscopic method, which can be used with dilute samples in aqueous buffer solutions. Here, we describe the basic procedure for recording an X-band EPR spectrum of a metalloprotein sample at low temperature. We also discuss basic optimization techniques to provide spectra with a high signal to noise ratio and minimum distortion. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - March 27, 2014 Category: Biochemistry Source Type: news
SPOT-Seq-RNA: Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction
RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein–RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein–RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, wit...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
3D-SURFER 2.: Web Platform for Real-Time Search and Characterization of Protein Surfaces
The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a sing...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Assessing the Quality of Modelled 3D Protein Structures Using the ModFOLD Server
Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
ITScorePro: An Efficient Scoring Program for Evaluating the Energy Scores of Protein Structures for Structure Prediction
One important component in protein structure prediction is to evaluate the free energy of a given conformation. Given the enormous number of possible conformations for a sequence, it is extremely challenging to quickly and accurately score the energies of these conformations and predict a reasonable structure within a practical computational time. Here, we describe an efficient program for energy evaluation, referred to as ITScorePro (Copyright © 2012). The energy scoring function in the ITScorePro program is based on the distance-dependent, pairwise atomic potentials for protein structure prediction that we recently ...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Direct Coupling Analysis for Protein Contact Prediction
During evolution, structure, and function of proteins are remarkably conserved, whereas amino-acid sequences vary strongly between homologous proteins. Structural conservation constrains sequence variability and forces different residues to coevolve, i.e., to show correlated patterns of amino-acid occurrences. However, residue correlation may result from direct coupling, e.g., by a contact in the folded protein, or be induced indirectly via intermediate residues. To use empirically observed correlations for predicting residue–residue contacts, direct and indirect effects have to be disentangled. Here we present mecha...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Modeling of Protein Side-Chain Conformations with RASP
Modeling of side-chain conformations on a fixed protein backbone, also called side-chain packing, plays an important role in protein structure prediction, protein design, molecular docking, and functional analysis. RASP, or RApid Side-chain Predictor, is a recently developed program that can model protein side-chain conformations with both high accuracy and high speed. Moreover, it can generate structures with few atomic clashes. This chapter first provides a brief introduction to the principle and performances of the RASP package. Then details on how to use RASP programs to predict protein side-chain conformations are ela...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
The MULTICOM Protein Tertiary Structure Prediction System
With the expansion of genomics and proteomics data aided by the rapid progress of next-generation sequencing technologies, computational prediction of protein three-dimensional structure is an essential part of modern structural genomics initiatives. Prediction of protein structure through understanding of the theories behind protein sequence–structure relationship, however, remains one of the most challenging problems in contemporary life sciences. Here, we describe MULTICOM, a multi-level combination technique, intended to predict moderate- to high-resolution structure of a protein through a novel approach of combi...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
RaptorX server: A Resource for Template-Based Protein Structure Modeling
We present a community-wide web-based protocol, RaptorX server (
http://raptorx.uchicago.edu
), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling. (Source: Springer protocols feed by Protein Science)
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
Protein Structure Modeling with MODELLER
Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence–structure gap. In this chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of al...
Source: Springer protocols feed by Protein Science - February 27, 2014 Category: Biochemistry Source Type: news
