Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR

Mayne, Leland; Paterson, Yvonne; Cerasoli, Douglas M.; Englander, S. Walter

doi:10.1021/bi00159a006

Cited by 71 publications

(78 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Comparing the log P values from Figure 2 to those for oxidized horse cytochrome c calculated from data given by Wand et al (1986), Paterson et al (1990), and Mayne et al (1992) indicates that the horse protein tends to exhibit larger P values than the C102T variant. This is in agreement with the observation that the horse protein exhibits a larger AGd at 300 K (Betz & Pielak, 1992).…”

Section: Jl Marmorino Et Almentioning

confidence: 70%

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

et al. 1993

View full text Add to dashboard Cite

Proton NMR spectroscopy was used to determine the rate constant, kobs, for exchange of labile protons in both oxidized (Fe(II1)) and reduced (Fe(I1)) iso-1-cytochrome c. We find that slowly exchanging backbone amide protons tend to lack solvent-accessible surface area, possess backbone hydrogen bonds, and are present in regions of regular secondary structure as well as in Q-loops. Furthermore, there is no correlation between k,, and the distance from a backbone amide nitrogen to the nearest solvent-accessible atom. These observations are consistent with the local unfolding model. Comparisons of the free energy change for denaturation, A G d , at 298 K to the free energy change for local unfolding, AG,, at 298 K for the oxidized protein suggest that certain conformations possessing higher free energy than the denatured state are detected at equilibrium. Reduction of the protein results in a general increase in AG,. Comparisons of AGd to AG, for the reduced protein show that the most open states of the reduced protein possess more structure than its chemically denatured form. This persistent structure in high-energy conformations of the reduced form appears to involve the axially coordinated heme.

show abstract

Section: Jl Marmorino Et Almentioning

confidence: 70%

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

et al. 1993

View full text Add to dashboard Cite

show abstract

“…PKA was prepared as described previously (15), and experiments were carried out in the presence of either ATP͞Mg 2ϩ or ATP͞Mg 2ϩ and a 2-fold M excess of PKI (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). PKI (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), which has a K d of 2 nM in the presence of 1 mM ATP and 5 mM Mg 2ϩ , was prepared as described (13). PKI(5-24) samples were dissolved with 6 l of D 2 O containing 20 mM ATP and 100 mM MgCl 2, pD 7.4.…”

Section: Methodsmentioning

confidence: 99%

“…of Health, Albany, NY) and was stored lyophilized at Ϫ20°C. Thrombin experiments were carried out with a 2.5-fold M excess of TMEGF (4)(5). TMEGF (4)(5), which has a K d of 120 nM, was prepared as described (16), stored lyophilized at Ϫ20°C, and dissolved by addition of 6 l of 25 mM TRIS in D 2 O, pD 7.9.…”

Section: Methodsmentioning

confidence: 99%

“…NMR has been the method most used to study protein-protein interactions by amide H͞D exchange since the first report in 1990 by Paterson et al (4). NMR studies of other protein-protein complexes have not yielded unambiguous identification of the interface because amide H͞D exchange rate variations also resulted from conformational changes (5)(6)(7)(8)(9)(10)(11). We propose that the key to separating conformational changes from interface information is to consider only those amides with rapid exchange rates in the uncomplexed state because these amides should be near the protein surface.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Identification of protein–protein interfaces by decreased amide proton solvent accessibility

Mandell

Falick²,

Komives³

1998

Proc. Natl. Acad. Sci. U.S.A.

200

214

View full text Add to dashboard Cite

Matrix-assisted laser desorption ionizationtime-of-f light mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. Amide hydrogens provide individualized probes along the entire protein sequence and measurements of amide proton [hydrogen͞deuterium (H͞D)] exchange rates have been used to analyze protein conformational changes, protein folding, and protein-protein interactions (1-3). NMR has been the method most used to study protein-protein interactions by amide H͞D exchange since the first report in 1990 by Paterson et al. (4). NMR studies of other protein-protein complexes have not yielded unambiguous identification of the interface because amide H͞D exchange rate variations also resulted from conformational changes (5-11). We propose that the key to separating conformational changes from interface information is to consider only those amides with rapid exchange rates in the uncomplexed state because these amides should be near the protein surface. An observed decrease in the exchange rate of a surface amide should primarily result from solvent accessibility changes, not from conformational changes. Information on the rapidly exchanging surface amides is nearly inaccessible by NMR because the surface amides exchange faster than the time required for measurement. In contrast, mass spectrometry is an ideal method to acquire information about decreased solvent accessibility of rapidly exchanging amides (12).Two protein-protein complexes were analyzed. The first was a complex of known structure, the catalytic subunit of murine cAMP-dependent protein kinase (PKA) complexed to the kinase inhibitor, PKI(5-24) (13). A complex of unknown structure was also analyzed, human ␣-thrombin bound to an 83-aa fragment of human thrombomodulin ]. The surfaces of PKA that interact with PKI(5-24) are consistent with the crystal structure of the complex. The results of the thrombin-TMEGF(4-5) complex are consistent with the structure of the complex between thrombin and a 19-aa peptide from TM (14) and provide new information about where this important anticoagulant protein directly contacts thrombin.

show abstract

“…HX is being used to define protein structures under extreme conditions as in loosely formed equilibrium molten globules at acid pH (Hughson et al, 1990;Kuroda et al, 1992;Chyan et al, 1993;Ptitsyn, 1995b), in organic solvents (Wu & Gorenstein, 1993), in the crystalline state (Pedersen et al, 1991;Gallagher et al, 1992) and even in the dry state (Desai et al, 1994). HX is being used to measure structure changes in complexes of proteins with massive chaperonins (Okazaki et al, 1994;Robinson et al, 1994;Zahn et al, 1994), with antibodies (Paterson et al, 1990;Mayne et al, 1992;Orban et al, 1994) and enzymes (Werner & Werner, 1992;Jones et al, 1993), in micelles (Thornton & Gorenstein, 1994), and even in whole active muscle (Rodgers et al, 1996).…”

mentioning

confidence: 99%

Hydrogen exchange: The modern legacy of Linderstrøm‐Lang

et al. 1997

View full text Add to dashboard Cite

This discussion, prepared for the Protein Society's symposium honoring the 100th anniversary of Kaj Linderstr~m-Lang, shows how hydrogen exchange approaches initially conceived and implemented by Lang and his colleagues some 50 years ago are contributing to current progress in structural biology. Examples are chosen from the active protein folding field. Hydrogen exchange methods now make it possible to define the structure of protein folding intermediates in various contexts: as tenuous molten globule forms at equilibrium under destabilizing conditions, in kinetic intermediates that exist for less than one second, and as infinitesimally populated excited state forms under native conditions. More generally, similar methods now find broad application in studies of protein structure, energetics, and interactions. This article considers the rise of these capabilities from their inception at the Carlsberg Labs to their contemporary role as a significant tool of modem structural biology.Keywords: cooperativity; folding intermediates; hydrogen exchange; Linderstrom-Lang; molten globule; protein foldingThe hydrogen exchange approach was conceived by Kaj Linderstram-Lang and implemented by him and his collaborators at the Carlsberg laboratories in the early 1950s. Pauling had just discovered the a-helix and P-sheet and postulated that they were stabilized by hydrogen bonds. In those exciting days at the dawn of modem protein science, Lang realized that peptide group NH hydrogens participate in continual exchange with the hydrogens of solvent, just as in the already understood polar side chains. He set out to test Pauling's ideas by measuring the exchange behavior of these hydrogens. Lang created entirely novel methods to measure H-D exchange, and together with his colleagues at the Carlsberg Labs, he studied hydrogen exchange in a number of proteins and peptides under various solution conditions (Hvidt & LinderstrgmLang, 1954, 1955a, 1955b Krause & Linderstrom-Lang, 1955;Linderstrom-Lang, 1955a, 1955b Berger & Linderstram-Lang, 1957; Benson & Linderstmm-Lang, 1959; Hvidt et ai., 1960). In comparison with modem capabilities the information available to Lang was severely limited in resolution and even in accuracy. Remarkably, he saw past these limitations and quickly moved past

show abstract

Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR

Cited by 71 publications

References 21 publications

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso‐1‐cytochrome c

Identification of protein–protein interfaces by decreased amide proton solvent accessibility

Hydrogen exchange: The modern legacy of Linderstrøm‐Lang

Contact Info

Product

Resources

About