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Topic: Protein NMR

    Note: these results are not from the primary (high quality) database.

ETH Zurich: Publications Membrane protein – lipid interactions in mixed micelles studied by NMR with the use of paramagnetic reagents. NMR characterization of the full-length recombinant murine prion protein, mPrP(23­231). NMR structure of the integral membrane protein OmpX. www.mol.biol.ethz.ch /groups/wider_group/publications   (2471 words)

Listmania! Protein Biochemistry books I need to buy The protein NMR bible - written by the man himself The other protein NMR bible, written by the good folks at Genentech NMR of Proteins and Nucleic Acids (Baker Lecture Series) www.amazon.com /exec/obidos/tg/listmania/list-browse/-/2HLZDR8UBQNJ6   (200 words)

CABM NMR Software Page SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. [1] Huang Y.J., Swapana, G.V., Rajan, P.K., Ke, H, Xia, B., Shukla, K., Inouye, M. and Montelione, G.T. Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli. www-nmr.cabm.rutgers.edu /NMRsoftware/nmr_software.html   (1240 words)

NMR & X-ray crystallography glossary Because of the strength of NMR in studying protein structure and function, NMR techniques are receiving renewed interest in pressure studies of proteins. Now it is becoming more common to use NMR for studies of ligand- binding conformations (i.e., a small molecule bound to a protein target). STD NMR of mixtures of potential ligands with as little as 1 nmol of protein yields 1D and 2D NMR spectra that exclusively show signals from molecules with binding affinity. www.genomicglossaries.com /content/nmr_email.asp   (5585 words)

CHEM 525 NMR Spectroscopy Protein NMR spectroscopy, sample NMR spectra of the protein ubiquitin Text (strongly recommended) : "Protein NMR Spectroscopy", J. Cavanagh, W.J. Fairbrother, A.G. Palmer III, N.J. Skelton (Academic Press, 1996). NMR parameters: pulse width, spectral width, dwell time, number of points, repetition delay, acquisition time, receiver gain, filter width, number of increments, transmitter frequency, transmitter power, decoupling power, Fourier transformation (size and apodization) bouman.chem.georgetown.edu /nmr/syllabus.htm   (195 words)

PDB: RCSB/Protein Data Bank Key words: Protein Data Bank, PDB, Macromolecular structure data, X-ray Crystallography, NMR. The Protein Data Bank is distributed in ISO 9660 format. Release 107U-EXP contains the experimental data, both x-ray structure factors (886) and NMR constraints (93), deposited between October 1, 2003 and January 1, 2004, on two CD_ROM disks. www.nist.gov /srd/nist80.htm   (247 words)

The Protein Data Bank and the challenge of structural genomics - Nature Structural & Molecular Biology PDB staff members are also participating in an analogous project, the Collaborative Computational Project for NMR (CCPN), which is just being initiated with the NMR community (http://www.bio.cam.ac.uk/nmr/ccp/). The Protein Data Bank and the challenge of structural genomics Data quality may be evaluated using the currently available validation server (http://pdb.rutgers.edu/validate) as well as new stereochemistry and experimental data checking tools that will be made available on the PDB web sites. www.nature.com /cgi-taf/DynaPage.taf?file=/nsmb/journal/v7/n11s/full/nsb1100_957.html   (2549 words)

Resumé Other activities include resolution of new membrane protein reconstitutions and functional characterizations in bilayers, the development and extensive use of novel solid state NMR and spin-label ESR methods to study protein structure and lipid-protein specificity in natural and reconstituted, fully functional membranes. Since returning to a faculty position in Oxford (1980), a very wide range of membrane systems and biophysical approaches, including novel solid state NMR methods, have been applied to the study of both lipids and proteins in model and fully functional natural membranes. A highly multidisciplinary approach has been adopted in the study of lipids in model and natural membranes which began with graduate work on liposomal and model systems (Leeds, 1972 - 1975), then post-doctoral research into the study of the molecular specificity of lipid-protein in membranes by ESR spin-label methods (Germany, 1976 - 1980). www2.bioch.ox.ac.uk /~awatts/resume.html   (588 words)

CHEM 525 NMR Spectroscopy Protein NMR spectroscopy, sample NMR spectra of the protein ubiquitin Text (strongly recommended) : "Protein NMR Spectroscopy", J. Cavanagh, W.J. Fairbrother, A.G. Palmer III, N.J. Skelton (Academic Press, 1996). NMR parameters: pulse width, spectral width, dwell time, number of points, repetition delay, acquisition time, receiver gain, filter width, number of increments, transmitter frequency, transmitter power, decoupling power, Fourier transformation (size and apodization) bouman.chem.georgetown.edu /nmr/syllabus.htm   (195 words)

Lecomte Lab Lecomte, J.T.J., De Marco, A., and Llinás, M. (1982) Analysis of the Methyl Proton NMR Spectrum of Crambin, a Hydrophobic Protein. Lecomte, J.T.J. and La Mar, G.N. (1987) 1H NMR Probe for Hydrogen Bonding of Distal Residues to Bound Ligands in Heme Proteins: Isotope Effect on Heme Electronic Structure of Myoglobin. De Marco, A., Lecomte, J.T.J., and Llinás, M. (1981) Solvent and Temperature Effects on Crambin, a Hydrophobic Protein, as Investigated by Proton Magnetic Resonance. research.chem.psu.edu /jtlgroup/publications.html   (1477 words)

Membrane Protein Folding We are pushing the envelope of what is currently possible for the structure determination of membrane proteins by NMR spectroscopy. Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. To this end, we are working to increase expression levels of membrane proteins and we are developing protocols to refold membrane proteins in lipid and detergent environments. www.faculty.virginia.edu /tamm/pages/project_folding.html   (405 words)

publ_rev_00_09.html In: Methods in Molecular Biology – Techniques in Protein NMR Vol. Watts, A., Straus, S.K., Grage, S., Kamihira, M., Lam, Y.-H. and Xhao, Z. (2003) Membrane protein structure determination using solid state NMR. Watts, A. and Opella, S.J. (2000) Membranes studied by NMR spectroscopy. www2.bioch.ox.ac.uk /~awatts/publ_rev_00_09.html   (207 words)

Solid-State NMR - Silk Project Due to the large molecular weight, the highly repetitive primary structure of the protein, and the heterogeneity of the solid protein (in our case the silk thread from spider and silkworm), the signals from the individual amino acids cannot be resolved in a solid-state NMR spectrum. Ultimately we would like to obtain a detailed structure of silks, on the length scales that NMR allows us to measure, to obtain a thorough understanding of the relationships between structure and properties in silk as this is still lacking. We are looking for solid-state NMR techniques that do not require spectral resolution and that are able to directly map the information that is being looked for. www.nmr.ethz.ch /research_projs/silk.html   (259 words)

NMR Software ANSIG is a program for viewing and assigning 2D, 3D and 4D NMR spectra (both homonuclear and heteronuclear) of biological macromolecules, mainly proteins. DASHA: Model-Free Analysis of Protein Dynamics from Heteronuclear NMR Relaxation Data, and DIFFC: Hydrodynamic calculations for proteins with known spatial structure - both developed at the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia; General advising - Prof. C NMR prediction engine available based on the analysis and correlation of over 2,017,000 observed chemical shifts and 81,000 coupling constants. www.spincore.com /nmrinfo/software_s.html   (1954 words)

Research highlights For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titration data were available. The structure determination of protein-protein complexes is a rather tedious and lengthy process, both by NMR and X-ray crystallography. Several methods based on docking to study protein complexes have been well developed over the past few years. www.nmr.chem.uu.nl /~abonvin/research.html   (1412 words)

Nuclear magnetic resonance - Wikipedia, the free encyclopedia Applications in which solid-state NMR effects occur are often related to structure investigations on membrane proteins, protein fibrils or all kinds of polymers, and chemical analysis in inorganic chemistry, but also include "exotic" applications like the plant leaves and fuel cells. NMR was first described independently by Felix Bloch and Edward Mills Purcell in 1946, (both of whom shared the Nobel Prize in physics in 1952 for their discovery). NMR studies a magnetic nucleus, like that of a hydrogen atom, by aligning it with an external magnetic field and perturbing this alignment using an electromagnetic field. en.wikipedia.org /wiki/Nuclear_magnetic_resonance   (3839 words)

NMR Group Bijvoet Center Utrecht X-ray crystallography and NMR spectroscopy are widely used to determine the structure of molecules up to the level of complex biological macromolecules such as proteins. Finally, the application of NMR in structural biology for the determination of protein structures will be illustrated by a visit of the NMR group at the Bijvoet Center for Biomolecular Structure. The theoretical course is concerned with the quantum mechanical basis of NMR spectroscopy and is concluded with an examination. www.nmr.chem.uu.nl /Education.html   (1499 words)

NMR Software NMR SIM™ is a spin dynamics simulation program which utilizes the standard 1D and 3D pulse sequences or appropriately modifies sequences to create a set of theoretical FIDs for user-defined spin systems. Icon NMR™ utilizes an intuitive symbol and menu based operation mode, featuring a high level of automation to simplify the setup and execution of a range of NMR experiments. It applies to 1D, 2D, 3D NMR, LC-NMR, UV, DAD, MS, tandem MS, LC-MS, FTMS data and molecules. www.bruker-biospin.com /nmr/products/software.html   (339 words)

e-NMR.com: Information on Nuclear Magnetic Resonance, X-ray Crystallography Technical barriers to NMR spectroscopy are diminishing and prospects are that NMR spectroscopy will eventually resolve protein structures up to 100,000 MW. Another special advantage of NMR spectroscopy is its sensitivity to motions on the time scale of most chemical events, allowing direct examination of motions on the millisecond to second range and indirect studies of motions on the nanosecond to microsecond range. Nuclear Magnetic Resonance (NMR) spectroscopy has a distinct advantage over X-ray crystallography in that crystallization, which is often difficult and sometimes impossible, is not necessary. www.e-nmr.com   (921 words)

Protein structure prediction - Wikipedia, the free encyclopedia The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences. Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure. Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. en.wikipedia.org /wiki/Protein_structure_prediction   (737 words)

Integral membrane protein - Wikipedia, the free encyclopedia Prepartion of perdeutrated membrane proteins and modern solution NMR techniques now enable studies of these larger structures through the application of the principles of transverse relaxation-optimized spectroscopy (TROSY). A transmembrane IMP is an integral membrane protein that spans from the internal to the external surface of the biological membrane or lipid bilayer in which it is embedded. Although the structures of thousands of proteins have become known by X-ray diffraction and Nuclear magnetic resonance, the structures of only a few dozens of integral membrane proteins are known at atomic resolution, because they tend to denature on removal from the membrane, under which condition they are impossible to analyze. en.wikipedia.org /wiki/Integral_membrane_protein   (603 words)

Nuclear magnetic resonance - Wikipedia, the free encyclopedia Applications in which solid-state NMR effects occur are often related to structure investigations on membrane proteins, protein fibrils or all kinds of polymers, and chemical analysis in inorganic chemistry, but also include "exotic" applications like the plant leaves and fuel cells. BMRB BioMagResBank - A repository for data from NMR spectroscopy of proteins, peptides, and nucleic acids. NMR studies a magnetic nucleus, like that of a hydrogen atom, protium being the most receptive isotope at natural abundance, by aligning it with a very powerful external magnetic field and perturbing this alignment using an electromagnetic field. en.wikipedia.org /wiki/Nuclear_magnetic_resonance   (3391 words)

NMR spectroscopy - Wikipedia, the free encyclopedia NMR spectroscopy is often the only way to obtain high resolution information on partially or wholly intrinsically unstructured proteins. Much of the recent innovation within NMR spectroscopy, has been within the field of protein NMR, which has become a very important technique in structural biology. NMR is based in quantum mechanical properties of nuclei, and as such is very reliable, predictable and reproducible. en.wikipedia.org /wiki/NMR_spectroscopy   (1571 words)

OCMS Links: NMR Links CYANA/DYANA - Software for NMR Protein Structure Determination Chem Tutor: NMR Tutorial - free downloadable program - gain experience in predicting proton and C-13 chemical shifts Please send any useful (or interesting) additions to Lindsay Battle, OCMS Information Officer www.ocms.ox.ac.uk /links/NMR.html   (48 words)

RFA-RM-04-026: Membrane Protein Production and Structure Determination Considerable research is ongoing in the area of membrane protein structure and function, yet relatively few investigators have applied the techniques of x-ray crystallography, electron diffraction, or NMR spectroscopy to study directly the structures of their proteins. Membrane proteins are the targets of a large number of pharmacologically and toxicologically active substances and are responsible, in part, for their uptake, metabolism, and clearance. Efficient methods are needed to characterize the functional state of the expressed and purified membrane proteins as well as their lipid and detergent contents, state of aggregation, physical homogeneity, and sequence microheterogeneity. grants.nih.gov /grants/guide/rfa-files/RFA-RM-04-026.html   (5811 words)

Protein Structure Literature Membrane proteins are greatly underrepresented in the Protein Data Bank because they are less amenable to the classical methods of X-ray crystallography and solution NMR. The evolutionary relationships of domains in proteins of known structure are described in the Structural Classification of Proteins (SCOP) database. A "new view" of proteins is presented based on the notion that conformational diversity for a single sequence may support multifunctionality, and that this in turn fosters relatively rapid evolution of function from existing folds. molvis.sdsc.edu /protexpl/favlit.htm   (2153 words)

ipedia.com: Protein structure prediction Article The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences. Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure. Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. www.ipedia.com /protein_structure_prediction.html   (542 words)

Molecular Modeling Factsheet Although most scientists choose high-priority structures as their targets, this theory provides the option to choose any one of the proteins within a family as the target, rather than trying to achieve experimental results using a protein that is particularly difficult to work with using crystallographic or NMR techniques. Target structures determined experimentally may then be further analyzed to evaluate their similarity to other known protein structures and to determine possible evolutionary relationships that are not identifiable from protein sequence alone. The secondary structure is generated by the folding of the primary sequence and refers to the path that the polypeptide backbone of the protein follows in space. www.ncbi.nlm.nih.gov /About/primer/molecularmod.html   (3790 words)

publications list   Insights into the structure and dynamics of unfolded proteins from NMR. Solution structure of the TAZ2 (CH3) domain of the transcriptional adaptor protein CBP. Alternative splicing of Wilms' tumor suppressor protein modulates DNA binding activity through isoform-specific DNA-induced conformational changes. www.scripps.edu /mb/dyson/publications_list.htm   (3790 words)

Radially Softening Diffusive Motions in a Globular Protein -- Dellerue et al. 81 (3): 1666 -- Biophysical Journal Dynamics of a globular protein as studied by neutron scattering and solid-state NMR. The characterization of internal diffusion in proteins is complicated by the variety of the motions present. The physical picture of a globular protein arising from the present analysis is as follows. www.biophysj.org /cgi/content/full/81/3/1666   (3790 words)

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