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Three-Dimensional Structure of the Apo Form of the N-Terminal EGF-like Module of Blood Coagulation Factor X As Determined by NMR Spectroscopy and Simulated Folding

Ullner, Magnus LU ; Selander, Maria; Persson, Egon; Stenflo, Johan LU ; Drakenberg, Torbjörn LU and Teleman, Olle (1992) In Biochemistry 31(26). p.5974-5983
Abstract

The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate peptide conformations by molecular dynamics simulation. The simulations used a novel functional form for the constraint potentials and were performed with two time steps to ensure rapid execution. Apart from preliminary runs to aid assignment of NOEs, 60 runs resulted in 13 accepted structures, which have two antiparallel β sheets, no α helices, and five tight turns. There is no hydrophobic cluster. The root mean square... (More)

The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate peptide conformations by molecular dynamics simulation. The simulations used a novel functional form for the constraint potentials and were performed with two time steps to ensure rapid execution. Apart from preliminary runs to aid assignment of NOEs, 60 runs resulted in 13 accepted structures, which have two antiparallel β sheets, no α helices, and five tight turns. There is no hydrophobic cluster. The root mean square deviation for the backbone of the 13 conformations is 0.65 ± 0.11 Å against their mean conformation. About half of the side chains have well-defined structure. The overall conformation is similar to that of murine EGF.

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organization
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Contribution to journal
publication status
published
subject
in
Biochemistry
volume
31
issue
26
pages
5974 - 5983
publisher
The American Chemical Society
external identifiers
  • scopus:0026630971
ISSN
0006-2960
DOI
language
English
LU publication?
yes
id
d6a7bd1e-6be1-46c6-8f4a-ef06076f7177
date added to LUP
2018-03-29 10:14:49
date last changed
2018-05-29 11:43:25
@article{d6a7bd1e-6be1-46c6-8f4a-ef06076f7177,
  abstract     = {<p>The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate peptide conformations by molecular dynamics simulation. The simulations used a novel functional form for the constraint potentials and were performed with two time steps to ensure rapid execution. Apart from preliminary runs to aid assignment of NOEs, 60 runs resulted in 13 accepted structures, which have two antiparallel β sheets, no α helices, and five tight turns. There is no hydrophobic cluster. The root mean square deviation for the backbone of the 13 conformations is 0.65 ± 0.11 Å against their mean conformation. About half of the side chains have well-defined structure. The overall conformation is similar to that of murine EGF.</p>},
  author       = {Ullner, Magnus and Selander, Maria and Persson, Egon and Stenflo, Johan and Drakenberg, Torbjörn and Teleman, Olle},
  issn         = {0006-2960},
  language     = {eng},
  month        = {02},
  number       = {26},
  pages        = {5974--5983},
  publisher    = {The American Chemical Society},
  series       = {Biochemistry},
  title        = {Three-Dimensional Structure of the Apo Form of the N-Terminal EGF-like Module of Blood Coagulation Factor X As Determined by NMR Spectroscopy and Simulated Folding},
  url          = {http://dx.doi.org/},
  volume       = {31},
  year         = {1992},
}