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Proteins in vacuo. A connection between mean overcrossing number and orientationally-averaged collision cross section

Reimann, Curt LU ; Arteca, GA and Tapia, O (2002) In Physical Chemistry Chemical Physics 4(16). p.4058-4064
Abstract
Recently, the structure of protein ions in vacuo has received a lot of interest. Experimentally, such structures can only be characterized by global, low-resolution descriptors like the orientationally-averaged collision cross section (σ) over bar. An alternative descriptor of chain entanglement, the mean overcrossing number (N) over bar, is a very useful tool because it can distinguish sensitively between different conformations based on aspects of their geometry and topology. An overcrossing number distribution arises from an ensemble of different projections of the protein structure onto a viewing plane, where for each projection, the number of crossings by the set of line segments joining sequence-adjacent Calpha atoms is computed. (N)... (More)
Recently, the structure of protein ions in vacuo has received a lot of interest. Experimentally, such structures can only be characterized by global, low-resolution descriptors like the orientationally-averaged collision cross section (σ) over bar. An alternative descriptor of chain entanglement, the mean overcrossing number (N) over bar, is a very useful tool because it can distinguish sensitively between different conformations based on aspects of their geometry and topology. An overcrossing number distribution arises from an ensemble of different projections of the protein structure onto a viewing plane, where for each projection, the number of crossings by the set of line segments joining sequence-adjacent Calpha atoms is computed. (N) over bar is the mean of this distribution. Despite their usefulness, overcrossing numbers depend on the atomic coordinates and thus cannot be measured for protein ions in vacuo as can collision cross sections. In this work, we explore theoretically whether collision cross sections are correlated with overcrossing numbers. Using a group of diverse proteins with the same chain length as lysozyme and known X-ray structures, we find a weak correlation between (σ) over bar and (N) over bar. Thus, a nontrivial range of orientationally-averaged cross section values can be consistent with the same mean overcrossing number. Since (N) over bar comprises a very sensitive tool for the study of conformational rearrangements, we checked also for correlations between (σ) over bar and (N) over bar during molecular dynamics simulated unfolding and relaxation pathways of lysozyme in vacuo. For a given pathway, the two quantities are found to be highly correlated. Although neither (σ) over bar nor (N) over bar maps one-to-one onto a particular tertiary fold, they are both sensitive descriptors to monitor the conformational state of a protein along a pathway of dynamical change. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Physical Chemistry Chemical Physics
volume
4
issue
16
pages
4058 - 4064
publisher
Royal Society of Chemistry
external identifiers
  • wos:000177201400018
  • scopus:0036037457
ISSN
1463-9084
DOI
10.1039/b200987k
language
English
LU publication?
yes
id
56d5b407-50b5-4051-81ed-a01e0737db16 (old id 332218)
date added to LUP
2007-11-12 09:57:17
date last changed
2017-01-01 06:44:15
@article{56d5b407-50b5-4051-81ed-a01e0737db16,
  abstract     = {Recently, the structure of protein ions in vacuo has received a lot of interest. Experimentally, such structures can only be characterized by global, low-resolution descriptors like the orientationally-averaged collision cross section (σ) over bar. An alternative descriptor of chain entanglement, the mean overcrossing number (N) over bar, is a very useful tool because it can distinguish sensitively between different conformations based on aspects of their geometry and topology. An overcrossing number distribution arises from an ensemble of different projections of the protein structure onto a viewing plane, where for each projection, the number of crossings by the set of line segments joining sequence-adjacent Calpha atoms is computed. (N) over bar is the mean of this distribution. Despite their usefulness, overcrossing numbers depend on the atomic coordinates and thus cannot be measured for protein ions in vacuo as can collision cross sections. In this work, we explore theoretically whether collision cross sections are correlated with overcrossing numbers. Using a group of diverse proteins with the same chain length as lysozyme and known X-ray structures, we find a weak correlation between (σ) over bar and (N) over bar. Thus, a nontrivial range of orientationally-averaged cross section values can be consistent with the same mean overcrossing number. Since (N) over bar comprises a very sensitive tool for the study of conformational rearrangements, we checked also for correlations between (σ) over bar and (N) over bar during molecular dynamics simulated unfolding and relaxation pathways of lysozyme in vacuo. For a given pathway, the two quantities are found to be highly correlated. Although neither (σ) over bar nor (N) over bar maps one-to-one onto a particular tertiary fold, they are both sensitive descriptors to monitor the conformational state of a protein along a pathway of dynamical change.},
  author       = {Reimann, Curt and Arteca, GA and Tapia, O},
  issn         = {1463-9084},
  language     = {eng},
  number       = {16},
  pages        = {4058--4064},
  publisher    = {Royal Society of Chemistry},
  series       = {Physical Chemistry Chemical Physics},
  title        = {Proteins in vacuo. A connection between mean overcrossing number and orientationally-averaged collision cross section},
  url          = {http://dx.doi.org/10.1039/b200987k},
  volume       = {4},
  year         = {2002},
}