WeNMR is a worldwide e-Infrastructure for NMR spectroscopy and structural biology. It is the largest virtual Organization in the life sciences and is supported by EGI.
WeNMR is a worldwide e-Infrastructure for NMR spectroscopy and structural biology. It is the largest virtual Organization in the life sciences and is supported by EGI.
WeNMR aims at bringing together complementary research teams in the structural biology and life science area into a virtual research community at a worldwide level and provide them with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the infrastructure is provided through a portal integrating commonly used software and GRID technology.
There are about 2 dozen computational NMR services available that can be divided into:
The three-year WeNMR project started in November 2010 as the natural successor of the eNMR project. Financial support was provided by the European Community grants 213010 (eNMR) and 261572 (WeNMR) in the 7th Framework Programme (e-Infrastructure RI-261571).
| Participant organisation name | Country |
|---|---|
| Universiteit Utrecht (BCBR) (Coordinator) | Netherlands |
| Johann Wolfgang Goethe Universitaet Frankfurt am Main (BMRZ) | Germany |
| Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) | Italy |
| Istituto Nazionale di Fisica Nucleare (INFN) | Italy |
| Radboud Universiteit Nijmegen (RUN) | Netherlands |
| University of Cambridge (UCAM ) | UK |
| European Molecular Biology Organization (EMBL) - Hamburg Outstation | Germany |
| Spronk NMR Consultancy SpronkNMR | Lithuania |
| Academia Sinica, Taipei | Taiwan |
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions, such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is the topic of the scientific field of structural biology, which employs techniques such as X-ray crystallography, NMR spectroscopy, cryo-electron microscopy (cryo-EM) and dual polarisation interferometry, to determine the structure of proteins.
Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated.
X-PLOR is a computer software package for computational structural biology originally developed by Axel T. Brunger at Yale University. It was first published in 1987 as an offshoot of CHARMM - a similar program that ran on supercomputers made by Cray Inc. It is used in the fields of X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins (NMR) analysis.
The residual dipolar coupling between two spins in a molecule occurs if the molecules in solution exhibit a partial alignment leading to an incomplete averaging of spatially anisotropic dipolar couplings.
The Journal of Biomolecular NMR publishes research on technical developments and innovative applications of nuclear magnetic resonance spectroscopy for the study of structure and dynamic properties of biopolymers in solution, liquid crystals, solids and mixed environments. Some of the main topics include experimental and computational approaches for the determination of three-dimensional structures of proteins and nucleic acids, advancements in the automated analysis of NMR spectra, and new methods to probe and interpret molecular motions.
Axel T. Brunger is a German American biophysicist. He is Professor of Molecular and Cellular Physiology at Stanford University, and a Howard Hughes Medical Institute Investigator. He served as the Chair of the Department of Molecular and Cellular Physiology (2013–2017).
In biomolecular structure, CING stands for the Common Interface for NMR structure Generation and is known for structure and NMR data validation.
Gerard Jacob Kleywegt is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank.
CS-ROSETTA is a framework for structure calculation of biological macromolecules on the basis of conformational information from NMR, which is built on top of the biomolecular modeling and design software called ROSETTA. The name CS-ROSETTA for this branch of ROSETTA stems from its origin in combining NMR chemical shift (CS) data with ROSETTA structure prediction protocols. The software package was later extended to include additional NMR conformational parameters, such as Residual Dipolar Couplings (RDC), NOE distance restraints, pseudocontact chemical shifts (PCS) and restraints derived from homologous proteins. This software can be used together with other molecular modeling protocols, such as docking to model protein oligomers. In addition, CS-ROSETTA can be combined with chemical shift resonance assignment algorithms to create a fully automated NMR structure determination pipeline. The CS-ROSETTA software is freely available for academic use and can be licensed for commercial use. A software manual and tutorials are provided on the supporting website https://csrosetta.chemistry.ucsc.edu/.
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.
GeNMR method is the first fully automated template-based method of protein structure determination that utilizes both NMR chemical shifts and NOE -based distance restraints.
CS23D is a web server to generate 3D structural models from NMR chemical shifts. CS23D combines maximal fragment assembly with chemical shift threading, de novo structure generation, chemical shift-based torsion angle prediction, and chemical shift refinement. CS23D makes use of RefDB and ShiftX.
The chemical shift index or CSI is a widely employed technique in protein nuclear magnetic resonance spectroscopy that can be used to display and identify the location as well as the type of protein secondary structure found in proteins using only backbone chemical shift data The technique was invented by David S. Wishart in 1992 for analyzing 1Hα chemical shifts and then later extended by him in 1994 to incorporate 13C backbone shifts. The original CSI method makes use of the fact that 1Hα chemical shifts of amino acid residues in helices tends to be shifted upfield relative to their random coil values and downfield in beta strands. Similar kinds of upfield and downfield trends are also detectable in backbone 13C chemical shifts.
Nuclear magnetic resonance chemical shift re-referencing is a chemical analysis method for chemical shift referencing in biomolecular nuclear magnetic resonance (NMR). It has been estimated that up to 20% of 13C and up to 35% of 15N shift assignments are improperly referenced. Given that the structural and dynamic information contained within chemical shifts is often quite subtle, it is critical that protein chemical shifts be properly referenced so that these subtle differences can be detected. Fundamentally, the problem with chemical shift referencing comes from the fact that chemical shifts are relative frequency measurements rather than absolute frequency measurements. Because of the historic problems with chemical shift referencing, chemical shifts are perhaps the most precisely measurable but the least accurately measured parameters in all of NMR spectroscopy.
Protein chemical shift re-referencing is a post-assignment process of adjusting the assigned NMR chemical shifts to match IUPAC and BMRB recommended standards in protein chemical shift referencing. In NMR chemical shifts are normally referenced to an internal standard that is dissolved in the NMR sample. These internal standards include tetramethylsilane (TMS), 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS) and trimethylsilyl propionate (TSP). For protein NMR spectroscopy the recommended standard is DSS, which is insensitive to pH variations. Furthermore, the DSS 1H signal may be used to indirectly reference 13C and 15N shifts using a simple ratio calculation [1]. Unfortunately, many biomolecular NMR spectroscopy labs use non-standard methods for determining the 1H, 13C or 15N “zero-point” chemical shift position. This lack of standardization makes it difficult to compare chemical shifts for the same protein between different laboratories. It also makes it difficult to use chemical shifts to properly identify or assign secondary structures or to improve their 3D structures via chemical shift refinement. Chemical shift re-referencing offers a means to correct these referencing errors and to standardize the reporting of protein chemical shifts across laboratories.
Randy John Read is a Wellcome Trust Principal Research Fellow and professor of protein crystallography at the University of Cambridge.
Hartmut Oschkinat is a German structural biologist and professor for chemistry at the Free University of Berlin. His research focuses on the study of biological systems with solid-state nuclear magnetic resonance.
Mei Hong is a Chinese-American biophysical chemist and professor of chemistry at the Massachusetts Institute of Technology. She is known for her creative development and application of solid-state nuclear magnetic resonance (ssNMR) spectroscopy to elucidate the structures and mechanisms of membrane proteins, plant cell walls, and amyloid proteins. She has received a number of recognitions for her work, including the American Chemical Society Nakanishi Prize in 2021, Günther Laukien Prize in 2014, the Protein Society Young Investigator award in 2012, and the American Chemical Society’s Pure Chemistry award in 2003.
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Gaetano T. Montelione is an American biophysical chemist, Professor of Chemistry and Chemical Biology, and Constellation Endowed Chair in Structural Bioinformatics at Rensselaer Polytechnic Institute in Troy, NY.