Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings - an assessment of the interrelation of NMR restraints

Pernille Rose Jensen, Jacob Bock Axelsen, Mathilde Hauge Lerche, Flemming M. Poulsen

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on (HN)-H-1-N-15 residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of (CO)-C-13-C-13(alpha) and N-15-(CO)-C-13 one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 Angstrom resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.
Original languageEnglish
JournalJournal of Biomolecular N M R
Volume28
Issue number1
Pages (from-to)31-41
ISSN0925-2738
DOIs
Publication statusPublished - 2004
Externally publishedYes

Keywords

  • Diazepam Binding Inhibitor
  • Hydrogen Bonding
  • Molecular Structure
  • Neural Cell Adhesion Molecules
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptides
  • Plant Proteins
  • Proteins
  • chymotrypsin inhibitor 2
  • Spectroscopy
  • Biochemistry, Genetics and Molecular Biology (all)
  • Biochemistry
  • Chymotrypsin inhibitor 2
  • Hydrogen bonds
  • NMR structures
  • Residual dipolar couplings
  • Structure refinement
  • carbon 13
  • hydrogen
  • nitrogen 15
  • article
  • calculation
  • computer program
  • controlled study
  • cross coupling reaction
  • geometry
  • hydrogen bond
  • molecular cloning
  • nuclear magnetic resonance spectroscopy
  • nuclear Overhauser effect
  • priority journal
  • protein folding
  • protein structure
  • proton nuclear magnetic resonance
  • BIOCHEMISTRY
  • SPECTROSCOPY
  • NEURAL CELL-ADHESION
  • COA-BINDING PROTEIN
  • 3-DIMENSIONAL STRUCTURE
  • PULSE SEQUENCES
  • CHEMICAL-SHIFTS
  • MOLECULAR-STRUCTURE
  • CRYSTAL-STRUCTURES
  • SCALAR COUPLINGS
  • DRUG DESIGN
  • DOMAIN
  • hydrogen bonds
  • residual dipolar couplings
  • structure refinement
  • Chemistry
  • Polymer Sciences
  • Animal Anatomy / Morphology / Histology
  • hydrogen bond geometry
  • NMR restraints interrelation
  • side-chain packing
  • chymotrypsin inhibitor 2 139466-47-0
  • proteins
  • 10060, Biochemistry studies - General
  • 10064, Biochemistry studies - Proteins, peptides and amino acids
  • NMR spectroscopy laboratory techniques, spectrum analysis techniques
  • structure calculations mathematical and computer techniques
  • X-ray crystallography crystallographic techniques, laboratory techniques
  • Biochemistry and Molecular Biophysics

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