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PROTEIN FOLD RECOGNITION THROUGH APPLICATION OF RESIDUAL DIPOLAR COUPLING DATA

Y. QU, J.-T. GUO, V. OLMAN, Y. XU
2003 Biocomputing 2004  
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for studying protein structures.  ...  analog, making it applicable to protein targets out of the scope of current protein threading techniques.  ...  Acknowledgments This work was funded in part by the Structural Biology Program of the Office of Health and Environmental Research, U.S. Department of Energy, under Contract No.  ... 
doi:10.1142/9789812704856_0043 fatcat:7ecybevvmzardoaeyn5w4qtum4

Solid state NMR studies of molecular recognition at protein–mineral interfaces

Gil Goobes, Patrick S. Stayton, Gary P. Drobny
2007 Progress in nuclear magnetic resonance spectroscopy  
NMR studies of the structure of the N-terminus of statherin as well as studies of the structures of peptides derived from the N-terminus were conducted by J.R. Long  ...  the role these residues play in surface recognition is of interest.  ...  The small folded core is created by the folding of the C-terminus helical region (33) (34) (35) (36) (37) (38) back onto the intermediate region through a loop region defined by proline residues.  ... 
doi:10.1016/j.pnmrs.2006.11.002 pmid:19768124 pmcid:PMC2746069 fatcat:4qrald4jizf6vgcwskinku2e7q

Nuclear Magnetic Resonance in the Era of Structural Genomics†

J. H. Prestegard, H. Valafar, J. Glushka, F. Tian
2001 Biochemistry  
The time required for structure determination by traditional NMR methods is currently long, but improved hardware, automation of analysis, and new sources of data such as residual dipolar couplings promise  ...  and the impact this methodology can have on structure determination of proteins.  ...  Fowler for his analysis of the ACP structure and Drs. J. W. Lee and E. Vysotski for their collaboration on the obelin samples.  ... 
doi:10.1021/bi0102095 pmid:11467927 fatcat:tfqzyvbswfevbjiahu3kdkd4ca

Dipolar couplings as a probe of molecular dynamics and structure in solution

Joel R Tolman
2001 Current Opinion in Structural Biology  
References and recommended reading Papers of particular interest, published within the annual period of review, have been highlighted as: • of special interest •• of outstanding interest  ...  Acknowledgements I thank Hashim Al-Hashimi for critical reading of the manuscript.  ...  The development of residual dipolar coupling methodology for the rapid recognition of homologous protein folds and for studies of submillisecond timescale dynamics has also seen considerable progress.  ... 
doi:10.1016/s0959-440x(00)00245-1 pmid:11785752 fatcat:5pvssmkvvbdipllaf5m227mls4

Protein backbone structure determination using only residual dipolar couplings from one ordering medium

M Andrec, P Du, R M Levy
2001 Journal of Biomolecular NMR  
Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein folds.  ...  In this paper, we describe an approach to the construction of protein backbone folds using experimental dipolar couplings based on a bounded tree search through a structural database.  ...  Acknowledgement This research was supported by the National Institutes of Health (NRSA Fellowship GM19856-02 to MA and grant GM-30580 to RML).  ... 
pmid:11824753 fatcat:kyq3jxwdujhnxdj2e5pcjaobui

Derivation of structural restraints using a thiol-reactive chelator

Alex Dvoretsky, Vadim Gaponenko, Paul R Rosevear
2002 FEBS Letters  
Recognition and identi¢cation of protein folds is a prerequisite for high-throughput structural genomics.  ...  Substitution of Yb 3+ , Mn 2+ , and Co 2+ permitted measurement of metal^amide proton distances, dipolar shifts, and residual dipolar couplings.  ...  Residual dipolar couplings RDCs for 1 H^1 5 N bond vectors have been shown to be an excellent tool for protein structure re¢nement [1, 18, 19] .  ... 
doi:10.1016/s0014-5793(02)03297-0 pmid:12297302 fatcat:2vlw6xh36zahhgk2stga3jg2ka

Structural Characterization of a Mannose-binding Protein–Trimannoside Complex using Residual Dipolar Couplings

Nitin U. Jain, Schroeder Noble, James H. Prestegard
2003 Journal of Molecular Biology  
The ligand-binding properties of a 53 kDa homomultimeric trimer from mannose-binding protein (MBP) have been investigated using residual dipolar couplings (RDCs) that are easily measured from NMR spectra  ...  of the ligand and isotopically labeled protein.  ...  Acknowledgements This work was supported by a grant from the National Institutes of Health (GM33225).  ... 
doi:10.1016/s0022-2836(03)00268-7 pmid:12691753 fatcat:v2r4gkexurcoljbhmpv2gy5xui

Protein Fold Family Recognition From Unassigned Residual Dipolar Coupling Data [article]

Rishi Mukhopadhyay, Paul Shealy, Homayoun Valafar
2019 arXiv   pre-print
In this paper we test a potential solution to these problems that we have called Probability Density Profile Analysis (PDPA) that utilizes unassigned residual dipolar coupling data that are relatively  ...  their ability to provide novel protein folds in recent years.  ...  Methods and Methods Residual Dipolar Couplings Residual dipolar couplings arise from the interaction between spin 1/2 nuclei (e.g.: 15 N-1 H) in strong magnetic fields according to equation 1 where the  ... 
arXiv:1911.00383v1 fatcat:f4zqfsr44zbutbae63dvf27md4

Bound-State Residual Dipolar Couplings for Rapidly Exchanging Ligands of His-Tagged Proteins

Ronald D. Seidel, Tiandi Zhuang, James H. Prestegard
2007 Journal of the American Chemical Society  
In principle, residual dipolar couplings (RDCs) provide a useful complement to NOE data in that they provide orientational constraints as opposed to distance constraints, but use in ligand binding applications  ...  The approach is validated through the observation of bound-state RDCs for the disaccharide, lactose, bound to the carbohydrate recognition domain of the mammalian lectin, Galectin-3  ...  Acknowledgements This work was supported by grant number GM33225 from the National Institutes of Health.  ... 
doi:10.1021/ja069145h pmid:17385862 pmcid:PMC2542485 fatcat:wxxpzlxhdvdn5kdvdee7fdktfi

Residual dipolar couplings: synergy between NMR and structural genomics

Hashim M Al-Hashimi, Dinshaw J Patel
2002 Journal of Biomolecular NMR  
The measurement of residual dipolar couplings in partially oriented systems and other new NMR methods will play an important role in this synergistic relationship between NMR and structural genomics.  ...  Both an expansion in the domain of NMR application, and important contributions to future structural genomics efforts can be anticipated.  ...  Acknowledgements We thank Dr Ananya Majumdar and Dr Joel Tolman for a critical reading of the manuscript. This research was supported by NIH Grants GM54777 and CA46778.  ... 
pmid:11885976 fatcat:yo4ncx4o35dsrb46c6gxcoltkm

NMR Spectroscopy Tools for Structure-Aided Drug Design

Steve W. Homans
2004 Angewandte Chemie International Edition  
The efficacy of this and other approaches for global-fold determination involving residual dipolar couplings is, however, likely to depend on topology.  ...  To see why this is the case, a brief digression into the theory of residual dipolar couplings is necessary.  ... 
doi:10.1002/anie.200300581 pmid:14705081 fatcat:sdi777ym3jgb3oeebyl3gv2sr4

NMR structures of biomolecules using field oriented media and residual dipolar couplings

J. H. Prestegard, H. M. Al-Hashimi, J. R. Tolman
2000 Quarterly Reviews of Biophysics (print)  
Protein structure refinement A number of protein structures have now been determined using a combination of residual dipolar coupling data and traditional NOE data.  ...  For example, 22 indicates a tetramer formed by first generating a dimer through a 2-fold rotation of a monomer, and second, generating a tetramer through another 2-fold rotation of the resulting dimer  ... 
doi:10.1017/s0033583500003656 pmid:11233409 fatcat:gllc2ynlhjaixpewp324qsldna

NMR dipolar couplings for the structure determination of biopolymers in solution

Eva de Alba, Nico Tjandra
2002 Progress in nuclear magnetic resonance spectroscopy  
Ramirez for kindly providing some of the ®gures used in this manuscript. We are also very grateful to James A. Ferretti for the careful reading of the manuscript and useful suggestions.  ...  Protein family search via dipolar couplings Residual dipolar couplings have been used to recognize protein folds in the pioneer work of Annila et al. [86] .  ...  Another example is the use of residual dipolar couplings and 15 N NMR relaxation data to identify protein residues that undergo conformational exchange [24] .  ... 
doi:10.1016/s0079-6565(01)00042-5 fatcat:lypcmqea6fho7pjoe4ctw2e6ra

Protein structure prediction using sparse dipolar coupling data

Y. Qu
2004 Nucleic Acids Research  
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies.  ...  The program correctly identi®ed structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.  ...  N± 1 H dipolar couplings are available'.  ... 
doi:10.1093/nar/gkh204 pmid:14744980 pmcid:PMC373331 fatcat:eoijnj7xhbdq5o2wpsy6rs4czu

Solution NMR of Large Molecules and Assemblies†

Mark P. Foster, Craig A. McElroy, Carlos D. Amero
2007 Biochemistry  
The advent of multidimensional (2D-4D) NMR, together with the widespread use of uniform isotopic labeling of proteins and RNA with the NMR-active isotopes, 15 N and 13 C, opened the door to detailed analyses  ...  Here we briefly describe the methodological advances that allow NMR spectroscopy of large macromolecules and their complexes and provide a perspective on the wide range of applications of NMR to biochemical  ...  Wilson (OSU) for critical reading of the manuscript.  ... 
doi:10.1021/bi0621314 pmid:17209543 pmcid:PMC2596980 fatcat:7r3fjm7j2rajfjzssjsmgsoqky
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