Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution

Wagner, Gerhard; Wüthrich, Kurt

doi:10.1016/0022-2836(82)90180-2

Cited by 328 publications

(87 citation statements)

References 38 publications

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“…We note that the mutants F22A, Y23A, N43G, and F45A in this region were reported to be highly destabilizing relative to the wild-type protein (46,47). A strong resistance to HX is observed to take place at -strands, in conformity with early NMR exchange measurements (48). This behavior, generally attributed to hydrogen bonding of amide protons in the -sheet, is captured here on the basis of local packing densities and tertiary contact distributions alone.…”

Section: Results and Comparison With Hx Experimentssupporting

confidence: 73%

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

et al. 1998

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Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the conformational fluctuations of proteins in their folded state. This so-called Gaussian network model (GNM) is applied here to the interpretation of experimental hydrogen exchange (HX) behavior of proteins in their native state or under weakly denaturing conditions. Calculations are performed for five proteins: bovine pancreatic trypsin inhibitor, cytochrome c, plastocyanin, staphylococcal nuclease, and ribonuclease H. The results are significant in two respects. First, a good agreement is reached between calculated fluctuations and experimental measurements of HX despite the simplicity of the model and within computational times 2 or 3 orders of magnitude faster than earlier, more complex simulations. Second, the success of a theory, based on the coupled conformational fluctuations of residues near the native state, to satisfactorily describe the native-state HX behavior indicates the significant contribution of local, but cooperative, fluctuations to protein conformational dynamics. The correlation between the HX data and the unfolding kinetics of individual residues further suggests that local conformational susceptibilities as revealed by the GNM approach may have implications relevant to the global dynamics of proteins.Hydrogen exchange (HX) data for proteins directly indicate the relative accessibility of various protons to solvent, typically under conditions that can be denaturing to different extents. Observed HX times can vary over extremely broad ranges, from instantaneous to months. Generally these various times have been interpreted and ascribed to several kinds of processesslocal fluctuations for the fastest, local unfolding for intermediate, and global unfolding for the slowest exchanges (1). Some disagreements have arisen between the descriptions of the underlying kinetic processes and the interpretation of HX mechanisms because of differences in the operational definitions of these processes (2). HX from native proteins was recently pointed out to monitor with a remarkable precision rapid conformational fluctuations of the order of microseconds to milliseconds, while no correlation could be observed between HX free energies of individual residues and their unfolding rates which are several orders of magnitude slower than local fluctuations (3). Global unfolding rates are expected to be the same for all residues, while the superimposed exchange rates due to residue fluctuations vary depending on local interactions (4, 1, 5). Here we will avoid ascribing rates to specific processes but instead investigate directly the extent of protection in the native state and compare this with the measured exchange rates. This analysis has become possible with the development of a new simple model of protein structure and dynamics, recently proposed for analyzing the conformational fluctuations of folded proteins (6, 7).Two limits, or two mechanisms of ex...

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Section: Results and Comparison With Hx Experimentssupporting

confidence: 73%

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

et al. 1998

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“…One involves a global or subglobal unfolding event (Englander and Kallenbach, 1983) and the other involves penetration of a solvent molecule into the protein structure and into proximity of the site of the amide group undergoing exchange (Miller and Dill, 1995;Dempsey, 2001). In the latter case, the so-called penetration model, hydrogen exchange between the protein and bulk solvent, is induced by the redistribution of interior hydrogen bonds or from the random association of pre-existing interior cavities (Nakanishi et al, 1973;Karplus and McCammon, 1981;Wagner and Wuthrich, 1982;Otting et al, 1991;Mayo and Baldwin, 1993). Thus, solvent "DeLano Scientific LLC….…”

Section: Mechanisms Of H/d Exchange In Proteinsmentioning

confidence: 99%

The extremely slow‐exchanging core and acid‐denatured state of green fluorescent protein

et al. 2008

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“…Two common models explain this response. In the "breathing" model used to explain the differences in hydrogen exchange rates observed in proteins, the amide protons become accessible to solvent due to transient local unfolding (Wagner & Wuthrich, 1982;Kuwajima & Baldwin, 1983;Wand et al, 1986;Englander et al, 1992). In the solvent penetration or diffusion model, protein amide hydrogens become exposed to solvent through small amplitude motions that form channels into the protein interior (Woodward & Rosenberg, 1971;Ellis et al, 1975;Woodward, 1977;Matthew & Richards, 1983;Tuchsen & Woodward, 1987).…”

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confidence: 99%

The orientation and dynamics of substance P in lipid environments

Keire

Kobayashi

1998

Protein Science

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The membrane-associated conformation of substance P (RPKPQQFFGLM-NH2) has been previously proposed to be the NKI-receptor-active conformation. In this work, NMR methods are applied to explore the orientation and dynamics of substance P at lipid surfaces for which the peptide's three-dimensional structure had been previously determined. Here the presence of dodecylphosphocholine (DPC) or sodium dodecylsulfate (SDS) micelles has been found to cause sequence specific changes in the acid-and base-catalyzed amide proton exchange rates relative to the solution state values. On binding of substance P to SDS micelles, the FFG portion showed the largest decreases in the base-catalyzed amide exchange rates. Similar sequence-specific changes in substance P are observed in the presence of DPC micelles, albeit at much weaker levels due to fast exchange between free and bound forms of the peptide. These differences are attributed to the location of the amide protons either in the surface double layer (via electrostatic effect) or inserted into the polar head group region of the micelles (via low dielectric). The sequence-specific effects of micelle association were also observed in the homonuclear nonselective spin-lattice relaxation time; these, in combination with spin-spin relaxation times, were used to calculate correlation times for the backbone amide protons. These data combined with paramagnetic broadening observations on peptide protons in the presence of spin-labeled lipids yield a detailed model of the interaction of substance P with lipid surfaces.Keywords: amide exchange; correlation times; dodecylphosphocholine; NMR; peptide-lipid interactions; sodium dodecylsulfate; substance P; TI and T2 relaxation Substance P (SP) is a member of the tachykinin family of neuropeptides and is widely distributed in both the central and peripheral nervous system of humans. Tachykinins, which are characterized by a common C-terminal tail (F-x-GLM-NH2 where x is F or V for mammals), are of biomedical interest because they have been shown to cause hypotension, contraction of smooth muscles, salivation, transmission of pain, and inflammation (Pernow, 1983). Ligands of SP receptors have potential as a novel class of anti-inflammatory or pain medication, and as a result, interest is high in the structural elements of the peptide that may control receptor activity and selectivity.The membrane-bound conformation of SP has been proposed to be the NK1 receptor active form (Schwyzer, 1995), and the three-dimensional structure of SP in the presence of Abbreviations: DPC, dodecylphosphocholine; RMSD, root-mean-square deviation; SDS, sodium dodecylsulfate; SP, substance P; 2D TOCSY, twodimensional total correlation spectroscopy. 1996). Both structures were similar, although fast exchange between free and bound forms was observed for SP with DPC micelles and predominantly bound characteristics were found for SP with SDS micelles.The three-dimensional SP structure at these lipid-membrane mimetics may represent either a receptor-bound co...

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Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution

Cited by 328 publications

References 38 publications

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

The extremely slow‐exchanging core and acid‐denatured state of green fluorescent protein

The orientation and dynamics of substance P in lipid environments

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