Trajectory analysis of NMR structure calculations

Daisuke Kohda, Fuyuhiko Inagaki

Research output: Contribution to journalArticle

Abstract

NMR as well as X-ray crystallography are used to determine the three-dimensional structures of macromolecules at atomic resolution. Structure calculation generates coordinates that are compatible with NMR data from randomly generated initial structures. We analyzed the trajectory taken by structures during NMR structure calculation in conformational space, assuming that the distance between two structures in conformational space is the root-mean-square deviation between the two structures. The coordinates of a structure in conformational space were obtained by applying the metric multidimensional scaling method. As an example, we used a 22-residue peptide, μ-Conotoxin GIIIA, and a simulated annealing protocol of XPLOR. We found that the three-dimensional solution of the multidimensional scaling analysis is sufficient to describe the overall configuration of the trajectories in conformational space. By comparing the trajectories of the entire calculation with those of the converged calculation, random sampling of conformational space is readily discernible. Trajectory analysis can also be used for optimization of protocols of NMR structure calculation, by examining individual trajectories.

Original languageEnglish
Pages (from-to)357-361
Number of pages5
JournalJournal of Biomolecular NMR
Volume5
Issue number4
DOIs
Publication statusPublished - Jun 1 1995

Fingerprint

Conotoxins
X Ray Crystallography
Trajectories
Nuclear magnetic resonance
Peptides
X ray crystallography
Simulated annealing
Macromolecules
Sampling

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

Cite this

Trajectory analysis of NMR structure calculations. / Kohda, Daisuke; Inagaki, Fuyuhiko.

In: Journal of Biomolecular NMR, Vol. 5, No. 4, 01.06.1995, p. 357-361.

Research output: Contribution to journalArticle

Kohda, Daisuke ; Inagaki, Fuyuhiko. / Trajectory analysis of NMR structure calculations. In: Journal of Biomolecular NMR. 1995 ; Vol. 5, No. 4. pp. 357-361.
@article{ecce3ce9f52440a4b0c84715f976cfee,
title = "Trajectory analysis of NMR structure calculations",
abstract = "NMR as well as X-ray crystallography are used to determine the three-dimensional structures of macromolecules at atomic resolution. Structure calculation generates coordinates that are compatible with NMR data from randomly generated initial structures. We analyzed the trajectory taken by structures during NMR structure calculation in conformational space, assuming that the distance between two structures in conformational space is the root-mean-square deviation between the two structures. The coordinates of a structure in conformational space were obtained by applying the metric multidimensional scaling method. As an example, we used a 22-residue peptide, μ-Conotoxin GIIIA, and a simulated annealing protocol of XPLOR. We found that the three-dimensional solution of the multidimensional scaling analysis is sufficient to describe the overall configuration of the trajectories in conformational space. By comparing the trajectories of the entire calculation with those of the converged calculation, random sampling of conformational space is readily discernible. Trajectory analysis can also be used for optimization of protocols of NMR structure calculation, by examining individual trajectories.",
author = "Daisuke Kohda and Fuyuhiko Inagaki",
year = "1995",
month = "6",
day = "1",
doi = "10.1007/BF00182278",
language = "English",
volume = "5",
pages = "357--361",
journal = "Journal of Biomolecular NMR",
issn = "0925-2738",
publisher = "Springer Netherlands",
number = "4",

}

TY - JOUR

T1 - Trajectory analysis of NMR structure calculations

AU - Kohda, Daisuke

AU - Inagaki, Fuyuhiko

PY - 1995/6/1

Y1 - 1995/6/1

N2 - NMR as well as X-ray crystallography are used to determine the three-dimensional structures of macromolecules at atomic resolution. Structure calculation generates coordinates that are compatible with NMR data from randomly generated initial structures. We analyzed the trajectory taken by structures during NMR structure calculation in conformational space, assuming that the distance between two structures in conformational space is the root-mean-square deviation between the two structures. The coordinates of a structure in conformational space were obtained by applying the metric multidimensional scaling method. As an example, we used a 22-residue peptide, μ-Conotoxin GIIIA, and a simulated annealing protocol of XPLOR. We found that the three-dimensional solution of the multidimensional scaling analysis is sufficient to describe the overall configuration of the trajectories in conformational space. By comparing the trajectories of the entire calculation with those of the converged calculation, random sampling of conformational space is readily discernible. Trajectory analysis can also be used for optimization of protocols of NMR structure calculation, by examining individual trajectories.

AB - NMR as well as X-ray crystallography are used to determine the three-dimensional structures of macromolecules at atomic resolution. Structure calculation generates coordinates that are compatible with NMR data from randomly generated initial structures. We analyzed the trajectory taken by structures during NMR structure calculation in conformational space, assuming that the distance between two structures in conformational space is the root-mean-square deviation between the two structures. The coordinates of a structure in conformational space were obtained by applying the metric multidimensional scaling method. As an example, we used a 22-residue peptide, μ-Conotoxin GIIIA, and a simulated annealing protocol of XPLOR. We found that the three-dimensional solution of the multidimensional scaling analysis is sufficient to describe the overall configuration of the trajectories in conformational space. By comparing the trajectories of the entire calculation with those of the converged calculation, random sampling of conformational space is readily discernible. Trajectory analysis can also be used for optimization of protocols of NMR structure calculation, by examining individual trajectories.

UR - http://www.scopus.com/inward/record.url?scp=34249753292&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34249753292&partnerID=8YFLogxK

U2 - 10.1007/BF00182278

DO - 10.1007/BF00182278

M3 - Article

C2 - 22911557

AN - SCOPUS:34249753292

VL - 5

SP - 357

EP - 361

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 4

ER -