Literature DB >> 19345125

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

Rishi Mukhopadhyay1, Xijiang Miao, Paul Shealy, Homayoun Valafar.   

Abstract

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.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19345125      PMCID: PMC4071621          DOI: 10.1016/j.jmr.2009.02.014

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  36 in total

1.  Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.

Authors:  H M Al-Hashimi; H Valafar; M Terrell; E R Zartler; M K Eidsness; J H Prestegard
Journal:  J Magn Reson       Date:  2000-04       Impact factor: 2.229

2.  Structural and dynamic analysis of residual dipolar coupling data for proteins.

Authors:  J R Tolman; H M Al-Hashimi; L E Kay; J H Prestegard
Journal:  J Am Chem Soc       Date:  2001-02-21       Impact factor: 15.419

3.  Graphical analysis of the relative orientation of molecular alignment tensors for a protein dissolved in two different anisotropic media.

Authors:  Kaoru Nomura; Masatsune Kainosho
Journal:  J Magn Reson       Date:  2002-01       Impact factor: 2.229

4.  BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank.

Authors:  Jurgen F Doreleijers; Steve Mading; Dimitri Maziuk; Kassandra Sojourner; Lei Yin; Jun Zhu; John L Markley; Eldon L Ulrich
Journal:  J Biomol NMR       Date:  2003-06       Impact factor: 2.835

5.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

Review 6.  Nuclear magnetic resonance structural studies of membrane proteins in micelles and bilayers.

Authors:  Xiao-Min Gong; Carla M Franzin; Khang Thai; Jinghua Yu; Francesca M Marassi
Journal:  Methods Mol Biol       Date:  2007

7.  A thorough dynamic interpretation of residual dipolar couplings in ubiquitin.

Authors:  Nils A Lakomek; Teresa Carlomagno; Stefan Becker; Christian Griesinger; Jens Meiler
Journal:  J Biomol NMR       Date:  2006-02       Impact factor: 2.835

8.  Estimation of relative order tensors, and reconstruction of vectors in space using unassigned RDC data and its application.

Authors:  Xijiang Miao; Rishi Mukhopadhyay; Homayoun Valafar
Journal:  J Magn Reson       Date:  2008-07-12       Impact factor: 2.229

9.  Order matrix analysis of residual dipolar couplings using singular value decomposition.

Authors:  J A Losonczi; M Andrec; M W Fischer; J H Prestegard
Journal:  J Magn Reson       Date:  1999-06       Impact factor: 2.229

10.  Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

Authors:  Hashim M Al-Hashimi; Yuying Gosser; Andrey Gorin; Weidong Hu; Ananya Majumdar; Dinshaw J Patel
Journal:  J Mol Biol       Date:  2002-01-11       Impact factor: 5.469

View more
  10 in total

1.  Structure and dynamics of the membrane-bound form of Pf1 coat protein: implications of structural rearrangement for virus assembly.

Authors:  Sang Ho Park; Francesca M Marassi; David Black; Stanley J Opella
Journal:  Biophys J       Date:  2010-09-08       Impact factor: 4.033

2.  Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings.

Authors:  Mikhail Simin; Stephanie Irausquin; Casey A Cole; Homayoun Valafar
Journal:  J Biomol NMR       Date:  2014-11-18       Impact factor: 2.835

3.  RDC derived protein backbone resonance assignment using fragment assembly.

Authors:  Xingsheng Wang; Brian Tash; John M Flanagan; Fang Tian
Journal:  J Biomol NMR       Date:  2010-12-30       Impact factor: 2.835

4.  Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.

Authors:  Paul Shealy; Mikhail Simin; Sang Ho Park; Stanley J Opella; Homayoun Valafar
Journal:  J Magn Reson       Date:  2010-07-30       Impact factor: 2.229

5.  Dynafold: a dynamic programming approach to protein backbone structure determination from minimal sets of Residual Dipolar Couplings.

Authors:  Rishi Mukhopadhyay; Stephanie Irausquin; Christopher Schmidt; Homayoun Valafar
Journal:  J Bioinform Comput Biol       Date:  2014-01-07       Impact factor: 1.122

6.  Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps.

Authors:  Sang Ho Park; Woo Sung Son; Rishi Mukhopadhyay; Homayoun Valafar; Stanley J Opella
Journal:  J Am Chem Soc       Date:  2009-10-14       Impact factor: 15.419

7.  REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.

Authors:  Casey A Cole; Nourhan S Daigham; Gaohua Liu; Gaetano T Montelione; Homayoun Valafar
Journal:  PLoS Comput Biol       Date:  2021-02-01       Impact factor: 4.475

8.  Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package.

Authors:  Casey Cole; Caleb Parks; Julian Rachele; Homayoun Valafar
Journal:  BMC Bioinformatics       Date:  2020-12-03       Impact factor: 3.169

9.  Advances in the REDCAT software package.

Authors:  Chris Schmidt; Stephanie J Irausquin; Homayoun Valafar
Journal:  BMC Bioinformatics       Date:  2013-10-07       Impact factor: 3.169

10.  Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

Authors:  Arjang Fahim; Rishi Mukhopadhyay; Ryan Yandle; James H Prestegard; Homayoun Valafar
Journal:  Molecules       Date:  2013-08-22       Impact factor: 4.411

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.