Efficient and accurate estimation of relative order tensors from lambda-maps.

The rapid increase in the availability of RDC data from multiple alignment media in recent years has necessitated the development of more sophisticated analyses that extract the RDC data's full information content. This article presents an analysis of the distribution of RDCs from two media (2D-RDC data), using the information obtained from a lambda-map. This article also introduces an efficient algorithm, which leverages these findings to extract the order tensors for each alignment medium using unassigned RDC data in the absence of any structural information. The results of applying this 2D-RDC analysis method to synthetic and experimental data are reported in this article. The relative order tensor estimates obtained from the 2D-RDC analysis are compared to order tensors obtained from the program REDCAT after using assignment and structural information. The final comparisons indicate that the relative order tensors estimated from the unassigned 2D-RDC method very closely match the results from methods that require assignment and structural information. The presented method is successful even in cases with small datasets. The results of analyzing experimental RDC data for the protein 1P7E are presented to demonstrate the potential of the presented work in accurately estimating the principal order parameters from RDC data that incompletely sample the RDC space. In addition to the new algorithm, a discussion of the uniqueness of the solutions is presented; no more than two clusters of distinct solutions have been shown to satisfy each lambda-map.

[1]  Homayoun Valafar,et al.  Tali: Local Alignment of protein Structures Using Backbone Torsion Angles , 2008, J. Bioinform. Comput. Biol..

[2]  Ad Bax,et al.  Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis. , 2008, The journal of physical chemistry. B.

[3]  A. Bax Weak alignment offers new NMR opportunities to study protein structure and dynamics , 2003, Protein science : a publication of the Protein Society.

[4]  J H Prestegard,et al.  Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings. , 2000, Journal of magnetic resonance.

[5]  Homayoun Valafar,et al.  REDCAT: a residual dipolar coupling analysis tool. , 2004, Journal of magnetic resonance.

[6]  G. Englert,et al.  High-Resolution Nuclear Magnetic Resonance Spectra of Orientated Molecules , 1963 .

[7]  Kenneth Levenberg A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[8]  Ke Ruan,et al.  De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media , 2008, Journal of biomolecular NMR.

[9]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[10]  Charles D Schwieters,et al.  The Xplor-NIH NMR molecular structure determination package. , 2003, Journal of magnetic resonance.

[11]  M. Levitt Spin Dynamics: Basics of Nuclear Magnetic Resonance , 2001 .

[12]  F. Marassi,et al.  Structures of the FXYD regulatory proteins in lipid micelles and membranes , 2007, Journal of bioenergetics and biomembranes.

[13]  Annaleen Vermeulen,et al.  Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings , 2000 .

[14]  William H. Press,et al.  Numerical recipes in C , 2002 .

[15]  A M Gronenborn,et al.  A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. , 1998, Journal of magnetic resonance.

[16]  Jun Zhu,et al.  BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank , 2003, Journal of biomolecular NMR.

[17]  J. Prestegard,et al.  Conformational differences in liganded and unliganded states of Galectin-3. , 2003, Biochemistry.

[18]  Homayoun Valafar,et al.  Rapid classification of a protein fold family using a statistical analysis of dipolar couplings , 2003, Bioinform..

[19]  A Nevzorov,et al.  Structure determination of membrane proteins by NMR spectroscopy. , 2002, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[20]  J. Cavanagh Protein NMR Spectroscopy: Principles and Practice , 1995 .

[21]  Homayoun Valafar,et al.  REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data. , 2008, Journal of magnetic resonance.

[22]  D. Patel,et al.  Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. , 2002, Journal of molecular biology.

[23]  D. Patel,et al.  Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings. , 2003, Journal of molecular biology.

[24]  J. Hus,et al.  Determination of protein backbone structure using only residual dipolar couplings. , 2001, Journal of the American Chemical Society.

[25]  Nuclear magnetic resonance structural studies of membrane proteins in micelles and bilayers. , 2007, Methods in molecular biology.

[26]  Rafael Brüschweiler,et al.  Self-consistency analysis of dipolar couplings in multiple alignments of ubiquitin. , 2003, Journal of the American Chemical Society.

[27]  Homayoun Valafar,et al.  Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application. , 2008, Journal of magnetic resonance.

[28]  Manuel Martin-Pastor,et al.  Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings. , 2002, Biopolymers.

[29]  Jens Meiler,et al.  A Thorough Dynamic Interpretation of Residual Dipolar Couplings in Ubiquitin , 2006, Journal of biomolecular NMR.

[30]  G. Hoatson,et al.  An Efficient Method for Calculating Powder Patterns , 1996, Journal of magnetic resonance. Series A.

[31]  J H Prestegard,et al.  NMR structures of biomolecules using field oriented media and residual dipolar couplings , 2000, Quarterly Reviews of Biophysics.

[32]  Homayoun Valafar,et al.  Rapid classification of protein structure models using unassigned backbone RDCs and probability density profile analysis (PDPA). , 2008, Journal of magnetic resonance.

[33]  H. Valafar,et al.  Backbone solution structures of proteins using residual dipolar couplings: Application to a novel structural genomics target , 2005, Journal of Structural and Functional Genomics.

[34]  J H Prestegard,et al.  Order matrix analysis of residual dipolar couplings using singular value decomposition. , 1999, Journal of magnetic resonance.

[35]  Ad Bax,et al.  Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. , 2003, Journal of the American Chemical Society.

[36]  P. Moore,et al.  A maximum likelihood method for determining D(a)(PQ) and R for sets of dipolar coupling data. , 2001, Journal of magnetic resonance.

[37]  Rafael Brüschweiler,et al.  Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J H Prestegard,et al.  Determination of protein backbone structures from residual dipolar couplings. , 2005, Methods in enzymology.

[39]  J H Prestegard,et al.  Structural and dynamic analysis of residual dipolar coupling data for proteins. , 2001, Journal of the American Chemical Society.

[40]  M. Blackledge Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings , 2005 .

[41]  C. Bush,et al.  Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings. , 2002, Carbohydrate research.

[42]  Ad Bax,et al.  The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase , 2000 .

[43]  Thomas F. Coleman,et al.  On the convergence of interior-reflective Newton methods for nonlinear minimization subject to bounds , 1994, Math. Program..