Hydrogen exchange in RNase A: neutron diffraction study.

Abstract

Hydrogen exchange has been studied in a single crystal of RNase A [ribonuclease (pancreatic), EC 3.1.27.5] in the course of a neutron structure investigation. Refinement of the occupancies of amide hydrogens provided information about the kind of isotope present in each site and also provided estimates of the errors associated with the measurement. Twenty-eight-of the 120 peptide amide hydrogens were found to be at least partially protected from exchange during approximately 1 year required for crystal preparation and data collection. Most of the protected hydrogens were involved in hydrogen bonds with main-chain carbonyl groups. A contiguous region of the fl-sheet containing residues 75, 106-109, 116, and 118 had a large number of protected hydrogens, indicating its low flexibility and the lack ofaccessibility to solvent. Residues 11-13 from, the a-helix near the amino, terminus were protected, in, good agreement with a model of cooperative unwinding ofthis helix, starting from the free (amino) end.The structure of a protein revealed by the techniques of x-ray or neutron diffraction is averaged over the time period of the data collection. However, some information about the dynamic states of the molecules is also accessible. An analysis of temperature factors may provide information about short-range vibrational and librational motions (1-3), and studies ofthe amide hydrogen exchange can provide information about long-range flexibility, in the different regions of the molecule. The latter technique is based on the observation that the exchange of either deuterium or tritium for amide hydrogens can pinpoint those areas that are both accessible to solvent and sufficiently flexible for the process to take place (4).Several methods of measuring the kinetics of hydrogen exchange in order to determine the conformational equilibria of single residues (5) have been reported. When, individual amide protons are well resolved in NMR spectra, as they are in the bovine pancreatic trypsin inhibitor (6, 7), their exchange kinetics can be determined. Another possibility is to monitor the degree of exchange by following the radioactive decay of the tritium label. Schreier and Baldwin (8) suggested that the special properties of RNase S make this protein a very suitable object for such studies. Their method involved labeling the S peptide (containing the first 20 residues from the amino terminus) with tritium and subsequently reforming an active enzyme by rapid mixing with the, remaining part of the molecule, which -consists of residues 21-124 (9). This technique yielded only the average rate of hydrogen exchange for the S peptide but still allowed the establishment ofa number of highly protected protons and showed that their individual exchange rates must be very similar. Rosa and Richards (10, 11) extended the resolution of this method by performing rapid proteolytic digestion and separating the fragments ofthe enzyme by high-pressure liquid chromatography. They were able to assign individual rates to a number of hydr...

Enhanced Prediction Accuracy of Protein Secondary Structure Using Hydrogen Exchange Fourier Transform Infrared Spectroscopy

“…Its chemical and physical mechanisms have been studied extensively (33)(34)(35)(36)(37)(38)(39)(40), and their impact has proven to be most valuable with deuterationsensitive spectroscopic methods such as IR (41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51), Raman (52), NMR (37,38,(53)(54)(55)(56)(57)(58)(59)(60)(61)(62), mass spectrometry (63)(64)(65)(66)(67)(68), and neutron diffraction (69).…”

A statistical mechanical model for hydrogen exchange in globular proteins

“…There is no obvious correlation between exchange rate and depth of burial in trypsin and ribonuclease (Kossiakoff, 1982;Wlodawer & Sjolin, 1982).…”

“…3. For intermediate and fast (non-&sheet) protons in BPTI, trypsin, and ribonuclease, there is no correlation between crystallographic B factors and exchange rates, suggesting that small internal fluctuations are not the primary mechanism of exchange (Levitt, 1981b;Kossiakoff, 1982;Wlodawer & Sjolin, 1982).…”

Neutron protein crystallography: beyond the folding structure of biological macromolecules

“…The general subject of neutron protein crystallography has been reviewed by several authors (Wlodawer, 1982;Schoenborn, 1985;Kossiakoff, 1985;Helliwell, 1997;Niimura, 1999;Tsyba & Bau, 2002;Niimura et al, 2006). Also of potential interest to readers are articles describing the synergy and complementarity between neutron diffraction and ultra-highresolution X-ray diffraction (Hazemann et al, 2005).…”