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Journal ArticleDOI

Primary Structure Effects on Peptide Group Hydrogen Exchange

01 Sep 1993-Proteins (NIH Public Access)-Vol. 17, Iss: 1, pp 75-86
TL;DR: The results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo‐ and polypeptides.
Abstract: The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest-neighbor blocking and inductive effects was tested in oligo- and polypeptides and, surprisingly, confirmed. Reference rates for alanine-containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured oligo- and polypeptides. The application of this approach to protein studies is discussed.
Citations
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Book ChapterDOI
TL;DR: It is predicted and confirmed experimentally that the molten globule state can exist in a living cell and plays an important role in a number of physiological processes.
Abstract: Publisher Summary This chapter describes the present state of the studies of the molten globule state and its role in protein folding and physiological processes Recent data on the intermediates (equilibrium and kinetic), focusing attention on the molten globule state are discussed in the chapter The molten globule has a native-like overall architecture (folding pattern) without including the rigid packing of side chains It is separated by first-order phase transitions from both the native and the unfolded states and represents a third thermodynamic state of protein molecules It is a universal kinetic intermediate in protein folding; the structure of this intermediate is similar to the structure of the equilibrium molten globule It is predicted and confirmed experimentally that the molten globule state can exist in a living cell and plays an important role in a number of physiological processes

1,163 citations

Journal ArticleDOI
TL;DR: The NMR structures of the recombinant human prion protein hPrP(23-230) include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered "tail," which influences the local conformational state of the polypeptide segments.
Abstract: The NMR structures of the recombinant human prion protein, hPrP(23–230), and two C-terminal fragments, hPrP(90–230) and hPrP(121–230), include a globular domain extending from residues 125–228, for which a detailed structure was obtained, and an N-terminal flexibly disordered “tail.” The globular domain contains three α-helices comprising the residues 144–154, 173–194, and 200–228 and a short anti-parallel β-sheet comprising the residues 128–131 and 161–164. Within the globular domain, three polypeptide segments show increased structural disorder: i.e., a loop of residues 167–171, the residues 187–194 at the end of helix 2, and the residues 219–228 in the C-terminal part of helix 3. The local conformational state of the polypeptide segments 187–193 in helix 2 and 219–226 in helix 3 is measurably influenced by the length of the N-terminal tail, with the helical states being most highly populated in hPrP(23–230). When compared with the previously reported structures of the murine and Syrian hamster prion proteins, the length of helix 3 coincides more closely with that in the Syrian hamster protein whereas the disordered loop 167–171 is shared with murine PrP. These species variations of local structure are in a surface area of the cellular form of PrP that has previously been implicated in intermolecular interactions related both to the species barrier for infectious transmission of prion disease and to immune reactions.

1,082 citations

Journal ArticleDOI
27 Feb 1997-Nature
TL;DR: Biophysical studies suggest that partly folded intermediates are involved in fibrillogenesis, and this may be relevant to amyloidosis generally.
Abstract: Tissue deposition of soluble proteins as amyloid fibrils underlies a range of fatal diseases. The two naturally occurring human lysozyme variants are both amyloidogenic, and are shown here to be unstable. They aggregate to form amyloid fibrils with transformation of the mainly helical native fold, observed in crystal structures, to the amyloid fibril cross-beta fold. Biophysical studies suggest that partly folded intermediates are involved in fibrillogenesis, and this may be relevant to amyloidosis generally.

1,028 citations

Journal ArticleDOI
14 Jul 1995-Science
TL;DR: The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.
Abstract: The hydrogen exchange behavior of native cytochrome c in low concentrations of denaturant reveals a sequence of metastable, partially unfolded forms that occupy free energy levels reaching up to the fully unfolded state. The step from one form to another is accomplished by the unfolding of one or more cooperative units of structure. The cooperative units are entire omega loops or mutually stabilizing pairs of whole helices and loops. The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.

981 citations

Journal ArticleDOI
TL;DR: The general principles of the hydrogen exchange coupled to mass spectrometry method are summarized, the latest variations on the experimental protocol that probe different types of protein movements are discussed, and other recent work and improvements in the field are reviewed.
Abstract: Hydrogen exchange coupled to mass spectrometry (MS) has become a valuable analytical tool for the study of protein dynamics. By combining information about protein dynamics with more classical functional data, a more thorough understanding of protein function can be obtained. In many cases, protein dynamics are directly related to specific protein functions such as conformational changes during enzyme activation or protein movements during binding. The method is made possible because labile backbone hydrogens in a protein will exchange with deuterium atoms when the protein is placed in a D2O solution. The subsequent increase in protein mass over time is measured with high-resolution MS. The location of the deuterium incorporation is determined by monitoring deuterium incorporation in peptic fragments that are produced after the labeling reaction. In this review, we will summarize the general principles of the method, discuss the latest variations on the experimental protocol that probe different types of protein movements, and review other recent work and improvements in the field. © 2005 Wiley Periodicals, Inc.

824 citations

References
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Journal ArticleDOI
TL;DR: In this article, a new mixing scheme based on the MLEV-16 composite pulse decoupling cycle (II) was proposed, which is less sensitive to pulse imperfections and provides net magnetization transfer over a substantial bandwidth with only limited rf power.

3,552 citations

Journal ArticleDOI
TL;DR: In this article, a pH meter reading in D/sub 2/O solutions was 0-40 pH unit lower than in H/sub O solutions, attributed to the glass electrode.
Abstract: Glass electrodes were used to measure the acidity in D/sub 2/O solution. A pH meter reading in D/sub 2/O solutions was 0-40 pH unit lower than in H/sub 2/ O solutions. This potential change was attributed to the glass electrode. (C.J.G.)

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Journal ArticleDOI
TL;DR: Strominger, J. L. H. (1960), Instruction Manual and Handbook, Beckman/Spinco Model 120 Amino Acid Analyzer, Palo Alto, California,Beckman Instruments Inc., Spinco Division.
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Journal ArticleDOI
TL;DR: The 2D NOE experiment has the principal advantage that it avoids detrimental effects arising from the limited selectivity of preirradiation in crowded spectral regions, and yields with a single instrument setting a complete network of NOE's between all the protons in the macromolecule.

1,842 citations