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Kumari P, Frey L, Sobol A, Lakomek NA, Riek R. 15N transverse relaxation measurements for the characterization of µs-ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange. JOURNAL OF BIOMOLECULAR NMR 2018; 72:125-137. [PMID: 30306288 DOI: 10.1007/s10858-018-0211-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
15N R2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based 15N R2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent 15N R2 rate constants-which should not be mistaken with protein inherent chemical exchange contributions, Rex, to 15N R2. For measurements of 15N R2 rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D2O molar fraction in the sample buffer, as low as 1%, or the use of an external D2O reference along with a modified 15N R2 Hahn-echo based experiment. This combination allows for the measurement of Rex contributions to 15N R2 originating from conformational exchange in a time window from µs to ms.
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Affiliation(s)
- Pratibha Kumari
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alexander Sobol
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Nils-Alexander Lakomek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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2
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Takeda M, Miyanoiri Y, Terauchi T, Yang CJ, Kainosho M. Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:148-154. [PMID: 24656087 DOI: 10.1016/j.jmr.2013.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 06/03/2023]
Abstract
Polar side-chains in proteins play important roles in forming and maintaining three-dimensional structures, and thus participate in various biological functions. Until recently, most protein NMR studies have focused on the non-exchangeable protons of amino acid residues. The exchangeable protons attached to polar groups, such as hydroxyl (OH), sulfhydryl (SH), and amino (NH2) groups, have mostly been ignored, because in many cases these hydrogen atoms exchange too quickly with water protons, making NMR observations impractical. However, in certain environments, such as deep within the hydrophobic interior of a protein, or in a strong hydrogen bond to other polar groups or interacting ligands, the protons attached to polar groups may exhibit slow hydrogen exchange rates and thus become NMR accessible. To explore the structural and biological implications of the interactions involving polar side-chains, we have developed versatile NMR methods to detect such cases by observing the line shapes of (13)C NMR signals near the polar groups, which are affected by deuterium-proton isotope shifts in a mixture of H2O and D2O. These methods allow the detection of polar side-chains with slow hydrogen-deuterium exchange rates, and therefore provide opportunities to retrieve information about the polar side-chains, which might otherwise be overlooked by conventional NMR experiments. Future prospects of applications using deuterium-proton isotope shifts to retrieve missing structural and dynamic information of proteins are discussed.
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Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yohei Miyanoiri
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tsutomu Terauchi
- Center for Priority Areas, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji 192-0397, Japan; SAIL Technologies Co., Inc., 1-40 Suehiro-cho 1-chome, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chun-Jiun Yang
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan; Center for Priority Areas, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji 192-0397, Japan.
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3
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Teze D, Hendrickx J, Dion M, Tellier C, Woods VL, Tran V, Sanejouand YH. Conserved Water Molecules in Family 1 Glycosidases: A DXMS and Molecular Dynamics Study. Biochemistry 2013; 52:5900-10. [DOI: 10.1021/bi400260b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- David Teze
- UFIP, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes,
France
| | - Johann Hendrickx
- UFIP, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes,
France
| | - Michel Dion
- UFIP, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes,
France
| | - Charles Tellier
- UFIP, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes,
France
| | - Virgil L. Woods
- Department of Medicine, University of California−San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0652, United States
| | - Vinh Tran
- UFIP, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes,
France
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4
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Gangadhara BN, Laine JM, Kathuria SV, Massi F, Matthews CR. Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein. J Mol Biol 2013; 425:1065-81. [PMID: 23333740 DOI: 10.1016/j.jmb.2013.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 01/01/2013] [Accepted: 01/03/2013] [Indexed: 01/31/2023]
Abstract
Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric enzyme that catalyzes consecutive reactions in imidazole biosynthesis through its HisF and HisH subunits. The unusually slow unfolding reaction of the isolated HisF TIM barrel domain from the thermophilic bacteria, Thermotoga maritima, enabled an NMR-based site-specific analysis of the main-chain hydrogen bonds that stabilize its native conformation. Very strong protection against exchange with solvent deuterium in the native state was found in a subset of buried positions in α-helices and pervasively in the underlying β-strands associated with a pair of large clusters of isoleucine, leucine and valine (ILV) side chains located in the α7(βα)8(βα)1-2 and α2(βα)3-6β7 segments of the (βα)8 barrel. The most densely packed region of the large cluster, α3(βα)4-6β7, correlates closely with the core of stability previously observed in computational, protein engineering and NMR dynamics studies, demonstrating a key role for this cluster in determining the thermodynamic and structural properties of the native state of HisF. When considered with the results of previous studies where ILV clusters were found to stabilize the hydrogen-bonded networks in folding intermediates for other TIM barrel proteins, it appears that clusters of branched aliphatic side chains can serve as cores of stability across the entire folding reaction coordinate of one of the most common motifs in biology.
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Affiliation(s)
- Basavanapura N Gangadhara
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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5
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Battistel MD, Shangold M, Trinh L, Shiloach J, Freedberg DI. Evidence for helical structure in a tetramer of α2-8 sialic acid: unveiling a structural antigen. J Am Chem Soc 2012; 134:10717-20. [PMID: 22703338 DOI: 10.1021/ja300624j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Characteristic H-bonding patterns define secondary structure in proteins and nucleic acids. We show that similar patterns apply for α2-8 sialic acid (SiA) in H(2)O and that H-bonds define its structure. A (15)N,(13)C α2-8 SiA tetramer, (SiA)(4), was used as a model system for the polymer. At 263 K, we detected intra-residue through-H-bond J couplings between (15)N and C8 for residues R-I-R-III of the tetramer, indicating H-bonds between the (15)N's and the O8's of these residues. Additional J couplings between the (15)N's and C2's of the adjacent residues confirm the putative H-bonds. NH groups showing this long-range correlation also experience slower (1)H/(2)H exchange. Additionally, detection of couplings between H7 and C2 for R-II and R-III implies that the conformations of the linkers between these residues are different than in the monomers. These structural elements are consistent with two left-handed helical models: 2 residues/turn (2(4) helix) and 4 residues/turn (1(4) helix). To discriminate between models, we resorted to (1)H,(1)H NOEs. The 2(4) helical model is in better agreement with the experimental data. We provide direct evidence of H-bonding for (SiA)(4) and show how H-bonds can be a determining factor for shaping its 3D structure.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, Maryland 20852-1448, USA
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Takeda M, Jee J, Ono AM, Terauchi T, Kainosho M. Hydrogen Exchange Study on the Hydroxyl Groups of Serine and Threonine Residues in Proteins and Structure Refinement Using NOE Restraints with Polar Side-Chain Groups. J Am Chem Soc 2011; 133:17420-7. [DOI: 10.1021/ja206799v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - JunGoo Jee
- Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji 192-0397, Japan
| | - Akira M. Ono
- Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji 192-0397, Japan
| | - Tsutomu Terauchi
- Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji 192-0397, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji 192-0397, Japan
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7
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Shaw BF, Arthanari H, Narovlyansky M, Durazo A, Frueh DP, Pollastri MP, Lee A, Bilgicer B, Gygi SP, Wagner G, Whitesides GM. Neutralizing positive charges at the surface of a protein lowers its rate of amide hydrogen exchange without altering its structure or increasing its thermostability. J Am Chem Soc 2010; 132:17411-25. [PMID: 21090618 DOI: 10.1021/ja9067035] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper combines two techniques--mass spectrometry and protein charge ladders--to examine the relationship between the surface charge and hydrophobicity of a representative globular protein (bovine carbonic anhydrase II; BCA II) and its rate of amide hydrogen-deuterium (H/D) exchange. Mass spectrometric analysis indicated that the sequential acetylation of surface lysine-ε-NH3(+) groups--a type of modification that increases the net negative charge and hydrophobicity of the surface of BCA II without affecting its secondary or tertiary structure--resulted in a linear decrease in the aggregate rate of amide H/D exchange at pD 7.4, 15 °C. According to analysis with MS, the acetylation of each additional lysine generated between 1.4 and 0.9 additional hydrogens that are protected from H/D exchange during the 2 h exchange experiment at 15 °C, pD 7.4. NMR spectroscopy demonstrated that none of the hydrogen atoms which became protected upon acetylation were located on the side chain of the acetylated lysine residues (i.e., lys-ε-NHCOCH3) but were instead located on amide NHCO moieties in the backbone. The decrease in rate of exchange associated with acetylation paralleled a decrease in thermostability: the most slowly exchanging rungs of the charge ladder were the least thermostable (as measured by differential scanning calorimetry). This observation--that faster rates of exchange are associated with slower rates of denaturation--is contrary to the usual assumptions in protein chemistry. The fact that the rates of H/D exchange were similar for perbutyrated BCA II (e.g., [lys-ε-NHCO(CH2)2CH3]18) and peracetylated BCA II (e.g., [lys-ε-NHCOCH3]18) suggests that the electrostatic charge is more important than the hydrophobicity of surface groups in determining the rate of H/D exchange. These electrostatic effects on the kinetics of H/D exchange could complicate (or aid) the interpretation of experiments in which H/D exchange methods are used to probe the structural effects of non-isoelectric perturbations to proteins (i.e., phosphorylation, acetylation, or the binding of the protein to an oligonucleotide or to another charged ligand or protein).
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Affiliation(s)
- Bryan F Shaw
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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8
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De Groot CO, Jelesarov I, Damberger FF, Bjelić S, Schärer MA, Bhavesh NS, Grigoriev I, Buey RM, Wüthrich K, Capitani G, Akhmanova A, Steinmetz MO. Molecular insights into mammalian end-binding protein heterodimerization. J Biol Chem 2009; 285:5802-14. [PMID: 20008324 DOI: 10.1074/jbc.m109.068130] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microtubule plus-end tracking proteins (+TIPs) are involved in many microtubule-based processes. End binding (EB) proteins constitute a highly conserved family of +TIPs. They play a pivotal role in regulating microtubule dynamics and in the recruitment of diverse +TIPs to growing microtubule plus ends. Here we used a combination of methods to investigate the dimerization properties of the three human EB proteins EB1, EB2, and EB3. Based on Förster resonance energy transfer, we demonstrate that the C-terminal dimerization domains of EBs (EBc) can readily exchange their chains in solution. We further document that EB1c and EB3c preferentially form heterodimers, whereas EB2c does not participate significantly in the formation of heterotypic complexes. Measurements of the reaction thermodynamics and kinetics, homology modeling, and mutagenesis provide details of the molecular determinants of homo- versus heterodimer formation of EBc domains. Fluorescence spectroscopy and nuclear magnetic resonance studies in the presence of the cytoskeleton-associated protein-glycine-rich domains of either CLIP-170 or p150(glued) or of a fragment derived from the adenomatous polyposis coli tumor suppressor protein show that chain exchange of EBc domains can be controlled by binding partners. Extension of these studies of the EBc domains to full-length EBs demonstrate that heterodimer formation between EB1 and EB3, but not between EB2 and the other two EBs, occurs both in vitro and in cells as revealed by live cell imaging. Together, our data provide molecular insights for rationalizing the dominant negative control by C-terminal EB domains and form a basis for understanding the functional role of heterotypic chain exchange by EBs in cells.
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Affiliation(s)
- Christian O De Groot
- Biomolecular Research, Structural Biology, the Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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9
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Takeda M, Jee J, Ono AM, Terauchi T, Kainosho M. Hydrogen Exchange Rate of Tyrosine Hydroxyl Groups in Proteins As Studied by the Deuterium Isotope Effect on Cζ Chemical Shifts. J Am Chem Soc 2009; 131:18556-62. [DOI: 10.1021/ja907911y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - JunGoo Jee
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - Akira Mei Ono
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - Tsutomu Terauchi
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center of Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
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10
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Durazo A, Shaw BF, Chattopadhyay M, Faull KF, Nersissian AM, Valentine JS, Whitelegge JP. Metal-free superoxide dismutase-1 and three different amyotrophic lateral sclerosis variants share a similar partially unfolded beta-barrel at physiological temperature. J Biol Chem 2009; 284:34382-9. [PMID: 19805550 DOI: 10.1074/jbc.m109.052076] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The structure and unfolding of metal-free (apo) human wild-type SOD1 and three pathogenic variants of SOD1 (A4V, G93R, and H48Q) that cause familial amyotrophic lateral sclerosis have been studied with amide hydrogen/deuterium exchange and mass spectrometry. The results indicate that a significant proportion of each of these proteins exists in solution in a conformation in which some strands of the beta-barrel (i.e. beta2) are well protected from exchange at physiological temperature (37 degrees C), whereas other strands (i.e. beta3 and beta4) appear to be unprotected from hydrogen/deuterium exchange. Moreover, the thermal unfolding of these proteins does not result in the uniform incorporation of deuterium throughout the polypeptide but involves the local unfolding of different residues at different temperatures. Some regions of the proteins (i.e. the "Greek key" loop, residues 104-116) unfold at a significantly higher temperature than other regions (i.e. beta3 and beta4, residues 21-53). Together, these results show that human wild-type apo-SOD1 and variants have a partially unfolded beta-barrel at physiological temperature and unfold non-cooperatively.
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Affiliation(s)
- Armando Durazo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, USA
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12
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Pearce FG. Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies. Biochem J 2006; 399:525-34. [PMID: 16822231 PMCID: PMC1615894 DOI: 10.1042/bj20060430] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 06/07/2006] [Accepted: 07/05/2006] [Indexed: 11/17/2022]
Abstract
During catalysis, all Rubisco (D-ribulose-1,5-bisphosphate carboxylase/oxygenase) enzymes produce traces of several by-products. Some of these by-products are released slowly from the active site of Rubisco from higher plants, thus progressively inhibiting turnover. Prompted by observations that Form I Rubisco enzymes from cyanobacteria and red algae, and the Form II Rubisco enzyme from bacteria, do not show inhibition over time, the production and binding of catalytic by-products was measured to ascertain the underlying differences. In the present study we show that the Form IB Rubisco from the cyanobacterium Synechococcus PCC6301, the Form ID enzyme from the red alga Galdieria sulfuraria and the low-specificity Form II type from the bacterium Rhodospirillum rubrum all catalyse formation of by-products to varying degrees; however, the by-products are not inhibitory under substrate-saturated conditions. Study of the binding and release of phosphorylated analogues of the substrate or reaction intermediates revealed diverse strategies for avoiding inhibition. Rubisco from Synechococcus and R. rubrum have an increased rate of inhibitor release. G. sulfuraria Rubisco releases inhibitors very slowly, but has an increased binding constant and maintains the enzyme in an activated state. These strategies may provide information about enzyme dynamics, and the degree of enzyme flexibility. Our observations also illustrate the phylogenetic diversity of mechanisms for regulating Rubisco and raise questions about whether an activase-like mechanism should be expected outside the green-algal/higher-plant lineage.
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Key Words
- ligand binding
- photosynthesis
- d-ribulose-1,5-bisphosphate carboxylase (rubisco)
- side reaction
- slow-binding inhibition
- carboxyarabinitol-1-p, 2′-carboxy-d-arabinitol 1-phosphate
- carboxyarabinitol-p2, 2′-carboxy-d-arabinitol 1,5-bisphosphate
- carboxypentitol-p2, unresolved isomeric mixture of carboxyarabinitol-p2 and 2′-carboxy-d-ribitol 1,5-bisphosphate
- carboxytetritol-p2, 2′-carboxy-d-tetritol 1,5-bisphosphate
- pentodiulose-p2, d-glycero-2,3-pentodiulose 1,5-bisphosphate
- p-glycerate, 3-phospho-d-glycerate
- p-glycolate, 2-phosphoglycolate
- ribulose-p2, d-ribulose 1,5-bisphosphate
- rubisco, d-ribulose-1,5-bisphosphate carboxylase/oxygenase
- xylulose-p2, d-xylulose 1,5-bisphosphate
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Affiliation(s)
- F Grant Pearce
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8020, New Zealand.
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13
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Barksdale AD, Rosenberg A. Acquisition and interpretation of hydrogen exchange data from peptides, polymers, and proteins. METHODS OF BIOCHEMICAL ANALYSIS 2006; 28:1-113. [PMID: 7048016 DOI: 10.1002/9780470110485.ch1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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14
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Polshakov VI, Birdsall B, Feeney J. Effects of co-operative ligand binding on protein amide NH hydrogen exchange. J Mol Biol 2005; 356:886-903. [PMID: 16405904 DOI: 10.1016/j.jmb.2005.11.084] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 11/24/2005] [Accepted: 11/28/2005] [Indexed: 11/28/2022]
Abstract
Amide protection factors have been determined from NMR measurements of hydrogen/deuterium amide NH exchange rates measured on assigned signals from Lactobacillus casei apo-DHFR and its binary and ternary complexes with trimethoprim (TMP), folinic acid and coenzymes (NADPH/NADP(+)). The substantial sizes of the residue-specific DeltaH and TDeltaS values for the opening/closing events in NH exchange for most of the measurable residues in apo-DHFR indicate that sub-global or global rather than local exchange mechanisms are usually involved. The amide groups of residues in helices and sheets are those most protected in apo-DHFR and its complexes, and the protection factors are generally related to the tightness of ligand binding. The effects of ligand binding that lead to changes in amide protection are not localised to specific binding sites but are spread throughout the structure via a network of intramolecular interactions. Although the increase in protein stability in the DHFR.TMP.NADPH complex involves increased ordering in the protein structure (requiring TDeltaS energy) this is recovered, to a large extent, by the stronger binding (enthalpic DeltaH) interactions made possible by the reduced motion in the protein. The ligand-induced protection effects in the ternary complexes DHFR.TMP.NADPH (large positive binding co-operativity) and DHFR.folinic acid.NADPH (large negative binding co-operativity) mirror the co-operative effects seen in the ligand binding. For the DHFR.TMP.NADPH complex, the ligand-induced protection factors result in DeltaDeltaG(o) values for many residues being larger than the DeltaDeltaG(o) values in the corresponding binary complexes. In contrast, for DHFR.folinic acid.NADPH, the DeltaDeltaG(o) values are generally smaller than many of those in the corresponding binary complexes. The results indicate that changes in protein conformational flexibility on formation of the ligand complex play an important role in determining the co-operativity in the ligand binding.
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Affiliation(s)
- Vladimir I Polshakov
- Division of Molecular Structure, National Institute for Medical Research The Ridgeway, Mill Hill London NW7 1AA, UK
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15
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Uchida K, Markley JL, Kainosho M. Carbon-13 NMR method for the detection of correlated hydrogen exchange at adjacent backbone peptide amides and its application to hydrogen exchange in five antiparallel beta strands within the hydrophobic core of Streptomyces subtilisin inhibitor (SSI). Biochemistry 2005; 44:11811-20. [PMID: 16128582 PMCID: PMC2631424 DOI: 10.1021/bi050467s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel method for monitoring proton-deuteron (H/D) exchange at backbone amides is based on the observation of H/D isotope effects on the (13)C NMR signals from peptide carbonyls. The line shape of the carbonyl (13)C(i) signal is influenced by differential H/D occupancy at the two adjacent amides: the H(N)(i)(+1) (beta site) and the H(N)(i) (gamma site). At a carbon frequency of 75.4 MHz, the H --> D isotope shifts on the (13)C signal are about 5-7 Hz for exchange at the beta site and 2 Hz or less for exchange at the gamma site. Because the effects at the two sites are additive, the time dependence of the line shape of a particular carbonyl resonance can report not only the exchange rates at the individual sites but also the level of dual exchange. Therefore, the data can be analyzed to determine the rate (k(c)) and degree of correlated exchange (X(betagamma)) at the two sites. We have applied this approach to the investigation of the pH dependence of hydrogen exchange at several adjacent residues in Streptomyces subtilisin inhibitor (SSI). Two selectively labeled SSI proteins were produced: one with selective (13)C' labeling at all valyl residues and one with selective (13)C' labeling at all leucyl residues. This permitted the direct observation by one-dimensional (13)C NMR of selected carbonyl signals from residues with slowly exchanging amides at the i and i + 1 positions. The residues investigated were located in an alpha helix and in a five-stranded antiparallel beta sheet. Samples of the two labeled proteins were prepared at various pH values, and (13)C NMR spectra were collected at 50 degrees C prior to and at various times after transferring the sample from H(2)O to (2)H(2)O. Most of the slowly exchanging amides studied were intramolecular hydrogen-bond donors. In agreement with prior studies, the results indicated that the exchange rates of the amide hydrogens in proteins are governed not only by hydrogen bonding but also by other factors. For example, the amide hydrogen of Thr34 exchanges rapidly even though it is an intramolecular hydrogen-bond donor. Over nearly the whole pH range studied, the apparent rates of uncorrelated exchange (k(beta) and k(gamma)) were proportional to [OH(-)] and the apparent rates of correlated exchange at two adjacent sites (k(c)) were roughly proportional to [OH(-)](2). This enabled us to extract the pH-independent exchange rates (k(beta) degrees , k(gamma) degrees , and k(c) degrees ). In all cases in which correlated exchange could be measured, the observed sigmoidal pH dependence of X(betagamma) could be replicated roughly from the derived pH-independent rates.
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Affiliation(s)
- Kenichi Uchida
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
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16
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Mazon H, Marcillat O, Forest E, Vial C. Hydrogen/deuterium exchange studies of native rabbit MM-CK dynamics. Protein Sci 2004; 13:476-86. [PMID: 14739330 PMCID: PMC2286700 DOI: 10.1110/ps.03380604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Creatine kinase (CK) isoenzymes catalyse the reversible transfer of a phosphoryl group from ATP onto creatine. This reaction plays a very important role in the regulation of intracellular ATP concentrations in excitable tissues. CK isoenzymes are highly resistant to proteases in native conditions. To appreciate localized backbone dynamics, kinetics of amide hydrogen exchange with deuterium was measured by pulse-labeling the dimeric cytosolic muscle CK isoenzyme. Upon exchange, the protein was digested with pepsin, and the deuterium content of the resulting peptides was determined by liquid chromatography coupled to mass spectrometry (MS). The deuteration kinetics of 47 peptides identified by MS/MS and covering 96% of the CK backbone were analyzed. Four deuteration patterns have been recognized: The less deuterated peptides are located in the saddle-shaped core of CK, whereas most of the highly deuterated peptides are close to the surface and located around the entrance to the active site. Their exchange kinetics are discussed by comparison with the known secondary and tertiary structures of CK with the goal to reveal the conformational dynamics of the protein. Some of the observed dynamic motions may be linked to the conformational changes associated with substrate binding and catalytic mechanism.
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Affiliation(s)
- Hortense Mazon
- UMR 5013 CNRS, Université Claude Bernard Lyon I, 43 boulevard du 11 Novembre 1918, 69622 Villeurbanne cedex, France
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17
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Russu IM. Probing Site-Specific Energetics in Proteins and Nucleic Acids by Hydrogen Exchange and Nuclear Magnetic Resonance Spectroscopy. Methods Enzymol 2004; 379:152-75. [PMID: 15051357 DOI: 10.1016/s0076-6879(04)79009-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Irina M Russu
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
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18
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Wüthrich K. Studies of static and dynamic aspects of spatial protein structures by high resolution nuclear magnetic resonance spectroscopy. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/macp.1981.020051981115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Hollecker M, Vincent M, Gallay J, Ruysschaert JM, Goormaghtigh E. Insight into the factors influencing the backbone dynamics of three homologous proteins, dendrotoxins I and K, and BPTI: FTIR and time-resolved fluorescence investigations. Biochemistry 2002; 41:15267-76. [PMID: 12484765 DOI: 10.1021/bi0204950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, combined with hydrogen/deuterium exchange technique and time-resolved fluorescence spectroscopy, has been used to investigate the changes in structure and dynamics that underlie the thermodynamic stability differences observed for three closely homologous proteins: dendrotoxins I and K, and bovine pancreatic trypsin inhibitor (BPTI). The experiments were performed on proteins under their native state and a modified form, obtained by selective reduction of a disulfide bond at the surface of the molecule, increasing slightly the backbone flexibility without changing the average structure. The data confirmed the high local as well as global rigidity of BPTI. In protein K, the exchange process was slow during the first 2 h of exchange, presumably reflecting a compact three-dimensional conformation, and then increased rapidly, the internal amide protons of the beta-strands exchanging 10-fold faster than in BPTI or protein I. The most probable destabilizing element was identified as Pro32, in the core of the beta-sheet. Protein I was found to present a 10% more expanded volume than protein K or BPTI, and there is a possible correlation between the resulting increased flexibility of the molecule and the lower thermodynamic stability observed for this protein. Interestingly, the interior amide protons of the beta-sheet structure were found to be as protected against exchange in protein I as in BPTI, suggesting that, although globally more flexible than that of Toxin K or BPTI, the structure of Toxin I could be locally quite rigid. The structural factors suspected to be responsible for the differences in internal flexibility of the two toxins could play a significant role in determining their functional properties.
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Affiliation(s)
- Michelle Hollecker
- Centre de Biophysique Moléculaire, UPR 4301 CNRS, affiliée Université Orléans et INSERM, Rue Charles-Sadron, 45071 Orléans Cedex 2, France.
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20
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Arrington CB, Robertson AD. Microsecond to minute dynamics revealed by EX1-type hydrogen exchange at nearly every backbone hydrogen bond in a native protein. J Mol Biol 2000; 296:1307-17. [PMID: 10698635 DOI: 10.1006/jmbi.2000.3536] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A previous comprehensive analysis of the pH dependence of native-state amide hydrogen (NH) exchange in turkey ovomucoid third domain (OMTKY3) yielded apparent opening and closing rate constants (k(op) and k(cl)) at 14 NH groups involved in global conformational changes. This analysis has been extended to 18 additional slowly exchanging NH groups. Quench-flow experiments were performed to monitor NH exchange in native OMTKY3 from neutral to very alkaline pH ( approximately 12) conditions. Above pH 10 the mechanism of exchange switched from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e. EX2 exchange), to one where exchange was limited by the rate of opening (i.e. EX1 exchange). Kinetics of solvent exposure are now known for nearly all backbone NH groups in native OMTKY3, yielding rate constants that span five orders of magnitude, 0.004 to 200 s(-1).
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Affiliation(s)
- C B Arrington
- Department of Biochemistry, the University of Iowa, Iowa City 52242, USA
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21
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Kraus M, Janek K, Bienert M, Krause E. Characterization of intermolecular beta-sheet peptides by mass spectrometry and hydrogen isotope exchange. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:1094-1104. [PMID: 10867683 DOI: 10.1002/1097-0231(20000715)14:13<1094::aid-rcm994>3.0.co;2-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The self-assembly of beta-sheet peptide domains resulting in the formation of fibrillar aggregates (amyloids) is a feature of various neurodegenerative disorders. In order to evaluate mass spectrometric methods for the characterization of intermolecular beta-sheet structures the hydrogen/deuterium exchange behaviour of model peptides DPKGDPKG-(VT)(n)-GKGDPKPD-amide (n = 3,4,5,6,7,8), (VT)(n)-peptides, composed of a central beta-sheet-forming domain and N- and C-terminal nonstructured octapeptide sequences, was measured by electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The kinetic analysis of the hydrogen/deuterium exchange (HX) shows that intermolecular beta-sheet structures contain slowly exchanging protons (k </=0.001 1/min). Localization of beta-sheet domains was achieved by monitoring the hydrogen exchange of peptide fragments generated via collision-induced dissociation (CID) or post source decay (PSD). The hydrogen exchange kinetics and the beta-sheet domains determined by ESI- and MALDI-MS were found to correlate with the length and stability of the beta-structure domain of the (VT)(n)-peptides.
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Affiliation(s)
- M Kraus
- Forschungsinstitut für Molekulare Pharmakologie, Alfred-Kowalke-Strasse 4, D-10315 Berlin, Germany.
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22
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Cavagnero S, Thériault Y, Narula SS, Dyson HJ, Wright PE. Amide proton hydrogen exchange rates for sperm whale myoglobin obtained from 15N-1H NMR spectra. Protein Sci 2000; 9:186-93. [PMID: 10739261 PMCID: PMC2144433 DOI: 10.1110/ps.9.1.186] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The hydrogen exchange behavior of exchangeable protons in proteins can provide important information for understanding the principles of protein structure and function. The positions and exchange rates of the slowly-exchanging amide protons in sperm whale myoglobin have been mapped using 15N-1H NMR spectroscopy. The slowest-exchanging amide protons are those that are hydrogen bonded in the longest helices, including members of the B, E, and H helices. Significant protection factors were observed also in the A, C, and G helices, and for a few residues in the D and F helices. Knowledge of the identity of slowly-exchanging amide protons forms the basis for the extensive quench-flow kinetic folding experiments that have been performed for myoglobin, and gives insights into the tertiary interactions and dynamics in the protein.
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Affiliation(s)
- S Cavagnero
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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23
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Kragelund BB, Heinemann B, Knudsen J, Poulsen FM. Mapping the lifetimes of local opening events in a native state protein. Protein Sci 1998; 7:2237-48. [PMID: 9827990 PMCID: PMC2143873 DOI: 10.1002/pro.5560071101] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The rate constants for the processes that lead to local opening and closing of the structures around hydrogen bonds in native proteins have been determined for most of the secondary structure hydrogen bonds in the four-helix protein acyl coenzyme A binding protein. In an analysis that combines these results with the energies of activation of the opening processes and the stability of the local structures, three groups of residues in the protein structure have been identified. In one group, the structures around the hydrogen bonds have frequent openings, every 600 to 1,500 s, and long lifetimes in the open state, around 1 s. In another group of local structures, the local opening is a very rare event that takes place only every 15 to 60 h. For these the lifetime in the open state is also around 1 s. The majority of local structures have lifetimes between 2,000 and 20,000 s and relatively short lifetimes of the open state in the range between 30 and 400 ms. Mapping of these groups of amides to the tertiary structure shows that the openings of the local structures are not cooperative at native conditions, and they rarely if ever lead to global unfolding. The results suggest a mechanism of hydrogen exchange by progressive local openings.
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Affiliation(s)
- B B Kragelund
- Carlsberg Laboratorium, Kemisk Afdeling, Valby, Copenhagen, Denmark
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24
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Nash DP, Jonas J. Structure of pressure-assisted cold denatured lysozyme and comparison with lysozyme folding intermediates. Biochemistry 1997; 36:14375-83. [PMID: 9398155 DOI: 10.1021/bi970881v] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
At high (> 3.5 kbar) pressures and low (< -10 degrees C) temperatures, hen egg-white lysozyme denatures readily and reversibly. Amide hydrogen exchange methods were used to investigate the structure of the pressure-assisted cold-denatured state of lysozyme. Protection factors were obtained for 52 backbone amide protons. The extent of protection of many of these protons is markedly different from that in lysozyme denatured by high temperature, high urea concentration, or chemical modification; specifically, the protection factors are higher and are strongly correlated with elements of secondary structure present in the native state. Furthermore, the pattern of protection factors is similar to that observed in lysozyme during refolding from highly denatured states, particularly during the early stages (< 3.5 ms) of refolding [Gladwin, S. T., & Evans, P. A. (1996) Folding Des. 1, 407]. Previous data on cold-denatured ribonuclease A were reevaluated and compared to known folding intermediates [Houry, W. A. & Scheraga, H. A. (1996) Biochemistry 35, 11734; Udgaonkar, J. B., & Baldwin, R. L. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 8197] to further test the supposition that the pressure-assisted cold-denatured states of proteins resemble the early folding stages.
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Affiliation(s)
- D P Nash
- Department of Chemistry, School of Chemical Sciences, University of Illinois at Urbana-Champaign 61801, USA
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25
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Abstract
This discussion, prepared for the Protein Society's symposium honoring the 100th anniversary of Kaj Linderstrøm-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 modern structural biology.
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Affiliation(s)
- S W Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104-6059, USA.
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26
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Morikis D, Wright PE. Hydrogen exchange in the carbon monoxide complex of soybean leghemoglobin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 237:212-20. [PMID: 8620875 DOI: 10.1111/j.1432-1033.1996.0212n.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hydrogen/deuterium exchange rates for individual amide protons have been measured for the carbon monoxide complex of soybean leghemoglobin. Fast two-dimensional NOESY experiments were performed, with 5.2-min data-collection time for each spectrum, which made possible the measurement of NOE cross-peaks of relatively rapidly exchanging amide protons at early time points. Exchange rates were measured for 61 backbone amides, the protection factors were calculated to provide information on the packing and local stability of the protein. The data are consistent with the presence of transient cooperative local unfolding of helical segments. The B-, E-, G- and H-helices have extensive regions of slow-, medium- and fast-exchanging amide protons. For each of these helices, there is a progressive decrease in protection on moving from the helix center to the termini. This is consistent with a stable helix center, with dynamic fraying at the ends. Amide exchange from the A-helix and C-helix is rapid except in small local regions. The F-helix, which is located on the proximal side of the heme pocket and is well formed in solution as demonstrated by characteristic medium range NOE connectivities [Morikis, D. Lepre, C.A. & Wright, P.E. (1994) Eur. J. Biochem. 219, 611-626], exhibits fast exchange for all amide protons. The implied flexibility and low stability of the F-helix may be functionally important in facilitating movement of the helix upon ligand binding. Fast exchange has also been observed for all amide protons in the CE-loop and in turns, as expected for flexible or solvent exposed regions. A strong tertiary contact has been established between the A-, G- and H-helices by the presence of a slowly exchanging indole N epsilon H of Trp129.
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Affiliation(s)
- D Morikis
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Swint-Kruse L, Robertson AD. Temperature and pH dependences of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 1996; 35:171-80. [PMID: 8555171 DOI: 10.1021/bi9517603] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two-dimensional nuclear magnetic resonance spectroscopy has been used to monitor proton-deuterium exchange rates (kobs) for more than 30 residues in turkey ovomucoid third domain. To test whether exchange is governed by global unfolding, rates were measured over a wide range of pH and temperatures where the change in the free energy of unfolding (delta Gzerou) is known [Swint, L., & Robertson, A. D. (1993) Protein Sci. 2, 2037-2049; Swint-Kruse, L., & Robertson, A. D. (1995) Biochemistry 34, 4724-4732]. Under conditions where EX2 kinetics are observed, a subset of 6-11 residues exhibits a one-to-one correlation with global stability. These residues are all located in central regions of secondary structures. Many other sites show varied degrees of correlation with delta Gzerou, while some are slower than expected on the basis of delta Gzerou alone. Preliminary evidence suggests that the latter is due to deviation from EX2 kinetics, even though experimental conditions are relatively mild (pH* 3 and 40 degrees C) compared to those in which deviations were observed for bovine pancreatic trypsin inhibitor. These results, together with similar observations for hen egg white lysozyme and barnase, suggest that EX2 kinetics should not be assumed when interpreting exchange studies.
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Affiliation(s)
- L Swint-Kruse
- Department of Biochemistry, University of Iowa, Iowa City 52242, USA
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28
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Abstract
We have analyzed the pH dependencies of published amide proton exchange rates (kex) in three proteins: bovine pancreatic trypsin inhibitor (BPTI), bull seminal plasma proteinase inhibitor IIA (BUSI IIA), and calbindin D9K. The base-catalyzed exchange rate constants (kOH) of solvent exposed amides in BPTI are lower for residues with low peptide carbonyl exposure, showing that the environment around the carbonyl oxygen influences kOH. We also examined the possible importance of an exchange mechanism that involves formations of imidic acid intermediates along chains of hydrogen-bonded peptides in the three proteins. By invoking this "relayed imidic acid exchange mechanism," which should be essentially acid-catalyzed, we can explain the surprisingly high pHmin (the pH value at which kex reaches a minimum) found for the non-hydrogen-bonded amide protons in the beta-sheet in BPTI. The successive increase of pHmin along a chain of hydrogen-bonded peptides from the free amide to the free carbonyl, observed in BPTI, can be explained as an increasing contribution of the proposed mechanism in this direction of the chain. For BUSI IIA (pH 4-5) and calbindin D9K (pH 6-7) the majority of amide protons with negative pH dependence of kex are located in chains of hydrogen-bonded peptides; this situation is shown to be consistent with the proposed mechanism.
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Affiliation(s)
- M A Eriksson
- Department of Biosciences, Karolinska Institute, Huddinge, Sweden
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29
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Andrec M, Hill RB, Prestegard JH. Amide exchange rates in Escherichia coli acyl carrier protein: correlation with protein structure and dynamics. Protein Sci 1995; 4:983-93. [PMID: 7663354 PMCID: PMC2143121 DOI: 10.1002/pro.5560040518] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The acyl carrier protein (ACP) of Escherichia coli is a 77-amino acid, highly negatively charged three-helix protein that plays a central role in fatty acid biosynthesis. Previous NMR studies have suggested the presence of multiple conformations and marginally stable secondary structural elements. The stability of these elements is now examined by monitoring amide exchange in apo-ACP using NMR-based methods. Because ACP exhibits many rapid exchange rates, application of traditional isotope exchange methods is difficult. In one approach, heteronuclear correlation experiments with pulsed field-gradient coherence selection have reduced the time needed to collect two-dimensional 1H-15N correlation spectra to the point where measurement of exchange of amide protons for deuterium on the timescale of minutes can be made. In another approach, water proton selective inversion-exchange experiments were performed to estimate the exchange rates of protons exchanging on timescales of less than a second. Backbone amide protons in the region of helix II were found to exchange significantly more rapidly than those in helices I and III, consistent with earlier structural models suggesting a dynamic disruption of the second helix. Highly protected amides occur on faces of the helices that may pack into a hydrophobic core present in a partially disrupted state.
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Affiliation(s)
- M Andrec
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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30
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Abstract
The hydrogen exchange (HX) rates of the slowest peptide group NH hydrogens in oxidized cytochrome c (equine) are controlled by the transient global unfolding equilibrium. These rates can be measured by one-dimensional nuclear magnetic resonance and used to determine the thermodynamic parameters of global unfolding at mild solution conditions well below the melting transition. The free energy for global unfolding measured by hydrogen exchange can differ from values found by standard denaturation methods, most notably due to the slow cis-trans isomerization of the prolyl peptide bond. This difference can be quantitatively calculated from basic principles. Even with these corrections, HX experiments at low denaturant concentration measure a free energy of protein stability that rises above the usual linear extrapolation from denaturation data, as predicted by the denaturant binding model of Tanford.
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Affiliation(s)
- Y Bai
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia 19104-6059
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31
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Affiliation(s)
- C Woodward
- Department of Biochemistry, University of Minnesota, St Paul 55108
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32
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Baldellon C, Padilla A, Cavé A. Kinetics of amide proton exchange in parvalbumin studied by 1H 2-D NMR. A comparison of the calcium and magnesium loaded forms. Biochimie 1992; 74:837-44. [PMID: 1334697 DOI: 10.1016/0300-9084(92)90066-n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The amide proton exchange rates have been measured for the pike parvalbumin loaded either with calcium (PaCa2) or with magnesium (PaMg2) by using 2-D total correlation spectroscopy experiments. The differences in the exchange rates observed between these two species were unexpected when compared with the small conformational changes induced in parvalbumin by the Ca/Mg exchange. With the calcium-loaded protein (PaCa2), a significant difference was observed for the amide proton exchange rates of residues located in the N-terminal domain AB in contrast to the slower exchange rates that were observed in the CD and EF domains. Such a difference does not exist for PaMg2, where faster exchange rates are observed over all the sequence. Since amide proton exchange rates are the signature of the solvent's accessibility in proteins, we interpreted our results in terms of difference of the equilibria between 'closed-states' and 'opened-states' for individual amide protons of the protein when calcium was replaced by magnesium. The CD and EF domains, and to a lesser extent the AB domain, would be more rigid when the protein was loaded with calcium ions. For the magnesium-loaded parvalbumin (PaMg2) the faster exchange rates we observed could be rationalized by a more flexible structure than in the case of the PaCa2.
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Affiliation(s)
- C Baldellon
- Centre CNRS-INSERM de Pharmacologie-Endocrinologie, Montpellier, France
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33
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Pedersen TG, Sigurskjold BW, Andersen KV, Kjaer M, Poulsen FM, Dobson CM, Redfield C. A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. J Mol Biol 1991; 218:413-26. [PMID: 2010918 DOI: 10.1016/0022-2836(91)90722-i] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Amide hydrogen/deuterium exchange behaviour has been studied for all of the peptide amides of hen lysozyme by means of two-dimensional n.m.r. spectroscopy. The amides have been grouped into four categories on the basis of their rates of exchange in solution at pH 4.2 and 7.5. The distribution of the amides into the different categories has been examined in the light of the crystallographic structural information, considering the type of secondary structure, the nature of hydrogen bonding and the distance from the protein surface. None of these features was found to determine uniquely the pattern of hydrogen exchange rates within the protein. The exchange behaviour of the individual amides could, however, in general be rationalized by a combination of these features. Hydrogen exchange was also monitored in both tetragonal and triclinic crystals of lysozyme, by allowing exchange to take place in the crystals prior to dissolution and recording of n.m.r. spectra under conditions where further exchange was minimized. This enabled direct comparison to be made of the exchange behaviour in the crystals and solution. A reduction in exchange rate was observed in the crystalline state relative to solution for a substantial number of amides and distinct differences between exchange in the different crystals could be observed. These differences between the solution and the different crystal states do not, however, correlate in a simple manner with proximity to intermolecular contacts in the crystals. However, the existence of these contacts, which are on the surface of the protein molecule, have a profound effect on the exchange of amides in the interior of the protein. The results indicate that the spectrum of fluctuations giving rise to hydrogen exchange may be significantly altered by the intermolecular interactions present within the crystalline state.
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Affiliation(s)
- T G Pedersen
- Kemisk Afdeling, Carlsberg Laboratorium, Valby, Copenhagen, Denmark
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34
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Lamerichs RM, Berliner LJ, Boelens R, De Marco A, Llinàs M, Kaptein R. Secondary structure and hydrogen bonding of crambin in solution. A two-dimensional NMR study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 171:307-12. [PMID: 3338468 DOI: 10.1111/j.1432-1033.1988.tb13791.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The secondary structure of crambin in solution has been determined using two-dimensional NMR and is found to be essentially identical to that of the crystal structure. The H-D exchange of most amide protons can be accounted for in terms of the hydrogen bonds found in the X-ray structure. Exceptions are the amide protons of Cys-4 and Ser-6, which exchange more slowly than expected, and of Asn-46 for which the exchange is faster. These results might be explained by a slightly different conformation of the C-terminal region of the protein in solution. The slow exchange of the amides of Cys-32 and Glu-23 might be due to aggregation involving an extremely hydrophobic part of the protein in solution.
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Affiliation(s)
- R M Lamerichs
- Department of Organic Chemistry, University of Utrecht, The Netherlands
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35
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36
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Abstract
The attempt is made to find new correlations between local structural characteristics of proteins and the hydrogen exchange rates of their individual main-chain amides, and to relate such correlations to possible mechanisms of hydrogen exchange. It is found that in bovine pancreatic trypsin inhibitor (BPTI) the surface area buried by a particular residue and its neighbors correlates with the exchange rate of the main-chain amide of that residue. As the area buried by a particular fragment can be associated with the stabilization of the protein structure by this fragment, the correlation suggests a role for the energetics of the local unfolding in the mechanism of hydrogen exchange. Calculations based on the assumption that the exchange mechanism involves local unfolding lead to quantitative agreement between the calculated and experimentally measured exchange rates for 80% of the amides of BPTI that are buried or hydrogen bonded to the main-chain or to internal water molecules. The same degree of correlation is found between the calculated exchange rates and partial exchange data for ribonuclease S, hen lysozyme and cytochrome c. A similarly strong correlation is found between calculated exchange rates and the exchange rates of ribonuclease A determined by neutron diffraction in the crystal. The criteria of correlation are, however, less stringent in this case because of the experimental errors, which are larger than for solution data. It is suggested that the observed correlation be used for predictions of hydrogen exchange rates in proteins.
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Affiliation(s)
- A A Rashin
- Department of Physiology & Biophysics, Mount Sinai School of Medicine, City University of New York, NY 10029
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37
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Wang QW, Kline AD, Wüthrich K. Amide proton exchange in the alpha-amylase polypeptide inhibitor Tendamistat studied by two-dimensional 1H nuclear magnetic resonance. Biochemistry 1987; 26:6488-93. [PMID: 2827730 DOI: 10.1021/bi00394a030] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The individual amide proton exchange rates in Tendamistat at pH 3.0 and 50 degrees C were measured by using two-dimensional 1H nuclear magnetic resonance. Overall, it was found that the distribution of exchange rates along the sequence is dominated by the interstrand hydrogen bonds of the beta-sheet structures. The slowly exchanging protons in the core of the two beta-sheets were shown to exchange via an EX2 mechanism. Further analysis of the data indicates that different large-scale structure fluctuations are responsible for the exchange from the two beta-sheets, even though the three-dimensional structure of Tendamistat appears to consist of a single structural domain.
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Affiliation(s)
- Q W Wang
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich-Hönggerberg, Switzerland
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38
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Wlodawer A, Deisenhofer J, Huber R. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. J Mol Biol 1987; 193:145-56. [PMID: 2438420 DOI: 10.1016/0022-2836(87)90633-4] [Citation(s) in RCA: 184] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The high resolution structures of bovine pancreatic trypsin inhibitor refined in two distinct crystal forms have been compared. One of the structures was a result of new least-squares X-ray refinement of data from crystal form I, while the other was the joint X-ray/neutron structure of crystal form II. After superposition, the molecules show an overall root-mean-squares deviation of 0.40 A for the atoms in the main chain, while the deviations for the side-chain atoms are 1.53 A. The latter number decreases to 0.61 A when those side-chains that adopted drastically different conformations are excluded from comparison. The discrepancy between atomic temperature factors in the two models was 6.7 A2, while their general trends are highly correlated. About half of the solvent molecules occupy similar positions in the two models, while the others are different. As expected, solvents with the lowest temperature factors are most likely to be common in the two crystal forms. While the two models are clearly similar, the differences are significantly larger than the errors inherent in the structure determination.
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39
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Segawa S, Kume K. Comparison between the unfolding rate and structural fluctuations in native lysozyme--effects of denaturants, ligand binding, and intrachain cross-linking on hydrogen exchange and unfolding kinetics. Biopolymers 1986; 25:1981-96. [PMID: 3779017 DOI: 10.1002/bip.360251012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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40
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Blake CC, Rice DW, Cohen FE. A "helix-scissors" mechanism for the hinge-bending conformational change in phosphoglycerate kinase. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1986; 27:443-8. [PMID: 3733317 DOI: 10.1111/j.1399-3011.1986.tb01040.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
X-ray studies of phosphoglycerate kinase (EC 2.7.2.3, PGK) have shown that the enzyme's single polypeptide chain is organized into two separate domains that correspond to the N- and C-terminal halves of the chain. Substrate binding studies and the incorporation of the complete amino acid sequence of horse-muscle PGK into its X-ray model suggest that the C-domain is an ADP/ATP binding unit and that the N-terminal domain contains the phosphoglycerate binding site and the active site located in a prominent cluster of positively charged residues. Because the distance between these two sites is 12-15 A, a hinge-bending of 10 degrees--20 degrees has been proposed to bring the two sites together for catalysis. Independent solution studies of yeast PGK have shown that the radius of gyration decreases significantly on the formation of the ternary complex. This change has been interpreted in terms of a 9 degrees--12 degrees rotation about a hinge in the interdomain region that brings the two domains together. We suggest here a structural basis for the proposed hinge-bending that involves the rotation of the two helices that form the domain interface about their contact normal carrying their respective domains with them.
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41
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Wagner G, Wüthrich K. Observation of internal motility of proteins by nuclear magnetic resonance in solution. Methods Enzymol 1986; 131:307-26. [PMID: 3773764 DOI: 10.1016/0076-6879(86)31047-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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42
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Abstract
The most correct model of the molecular structure of a protein molecule is one which describes it as having a number of variable conformational states. These states differ in degree over a large spectrum of structural variation ranging from individual atomic vibrational motion to significant tertiary denaturation. The application of the neutron diffraction techniques discussed above dealt with two classes of conformational fluctuation, "protein breathing" and "regional melting." The utility of the neutron technique stems from the ability to locate hydrogen atoms and to discriminate between hydrogens and deuteriums. This latter attribute allows for performing H/D exchange experiments by identifying individual sites of exchange. With this information it has been possible to discern which regions of the protein molecule undergo regional melting. Protein breathing was explored by analyzing the rotational properties of side chain methyl groups. Such information clearly suggested that most of these groups reside in "staggered" (low energy) conformation in the time averaged structure and are not greatly affected by local structural packing. Together these two classes of conformational fluctuation span nearly the full range of all motions that might play a role in biological activity. Information about such motions can be obtained from other types of physicochemical methods, but in most cases the interpretation of the data is considerably less definitive than that which can be obtained from a neutron analysis.
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43
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Gregory RB, Rosenberg A. Protein conformational dynamics measured by hydrogen isotope exchange techniques. Methods Enzymol 1986; 131:448-508. [PMID: 3022109 DOI: 10.1016/0076-6879(86)31052-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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44
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Kumar NV, Kallenbach NR. Hydrogen exchange of individual amide protons in the F helix of cyanometmyoglobin. Biochemistry 1985; 24:7658-62. [PMID: 3004560 DOI: 10.1021/bi00347a024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrogen exchange of the individual amide protons of alanine-90 (F5), glutamine-91 (F6), serine-92 (F7), and histidine-93 (F8) residues in cyanometmyoglobin of sperm whale has been studied by 1H nuclear magnetic resonance spectroscopy at 360 MHz. The amide proton resonance of F5, F6, and F7 have been assigned by use of the selective nuclear Overhauser effect between the consecutive amide protons. At pH 6.8, and in the temperature range of 5-20 degrees C, these protons show a 10(4)-fold retardation compared to the rates in free peptides. Apparent activation enthalpies for hydrogen exchange of F5, F6, and F8 protons are 18.5 +/- 0.4, 9.5 +/- 0.3, and 18.5 +/- 0.3 kcal/mol, respectively. Some implications of these results on the nature of the opening processes involved in hydrogen exchange are considered.
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45
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Wagner G, Stassinopoulou CI, Wüthrich K. Amide-proton exchange studies by two-dimensional correlated 1H NMR in two chemically modified analogs of the basic pancreatic trypsin inhibitor. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 145:431-6. [PMID: 6209139 DOI: 10.1111/j.1432-1033.1984.tb08572.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The backbone amide proton exchange with the solvent was investigated in 2H2O solutions of the basic pancreatic trypsin inhibitor and two chemical modifications thereof, which were obtained by transamination of the N-terminus and by cleavage of the disulfide bond 14-38, respectively. The three proteins have nearly identical conformations, but the stability with respect to thermal denaturation is markedly different. Exchange rates for a large number of individually assigned amide protons located both in central and peripheral parts of the protein structures were measured by two-dimensional correlated spectroscopy (COSY). From analysis of the individual proton exchange rates in the three proteins at different temperatures, an interplay of global and local structure fluctuations was characterized, which promote hydrogen exchange in distinct regions of the molecules. The exchange of particular amide protons may be governed by different motional processes at different temperatures. As a general trend, global fluctuations involving breakage of numerous hydrophilic secondary bonds appear to be dominant at higher temperatures, whereas at lower temperatures the influence of local fluctuations in hydrophobic regions of the protein structures is also clearly noticeable.
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46
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Stassinopoulou CI, Wagner G, Wüthrich K. Two-dimensional 1H NMR of two chemically modified analogs of the basic pancreatic trypsin inhibitor. Sequence-specific resonance assignments and sequence location of conformation changes relative to the native protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 145:423-30. [PMID: 6209138 DOI: 10.1111/j.1432-1033.1984.tb08571.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Two-dimensional nuclear magnetic resonance was used to obtain sequence specific assignments for the 1H NMR spectra of two chemically modified analogs of the basic pancreatic trypsin inhibitor. In one analog the disulfide bond 14-38 was cleaved, in the second derivative the N-terminus was transaminated. From measurements of the chemical shifts and determination of the sequence locations of slowly exchanging backbone amide protons it was found that conformational differences between the native inhibitor and the chemical modifications occur exclusively near the modification sites and that the internal hydrogen bonds are nearly fully preserved. Intriguing conformation differences with respect to the native protein are that for five residues in the transaminated inhibitor and for one residue in the reduced inhibitor multiple local conformers are indicated, and that the four internal water molecules observed in the crystal structure of the native inhibitor appear not to be preserved after reduction of the disulfide bond 14-38.
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47
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Tainer JA, Getzoff ED, Alexander H, Houghten RA, Olson AJ, Lerner RA, Hendrickson WA. The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature 1984; 312:127-34. [PMID: 6209578 DOI: 10.1038/312127a0] [Citation(s) in RCA: 400] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
To study the nature of antigenic recognition, antibodies have been prepared against a set of peptide sequences representing both highly mobile and well-ordered regions of myohaemerythrin, based on X-ray crystallographic temperature factors. Anti-peptide antibodies against highly mobile regions react strongly with the native protein; anti-peptide antibodies from well-ordered regions do not. Mobility is a major factor in the recognition of the native protein by anti-peptide antibodies; this may be of general significance in protein-protein interactions.
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48
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Bonnet D, Marden MC, Begard E, Hoa GH, Douzou P. Tritium exchange of spectrin versus temperature. Biopolymers 1984; 23:2587-602. [PMID: 6518266 DOI: 10.1002/bip.360231130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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49
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Wüthrich K, Strop P, Ebina S, Williamson MP. A globular protein with slower amide proton exchange from an alpha helix than from antiparallel beta sheets. Biochem Biophys Res Commun 1984; 122:1174-8. [PMID: 6477556 DOI: 10.1016/0006-291x(84)91215-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In proteinase inhibitor IIA from bull seminal plasma, which is a small globular protein with 57 amino acid residues, measurements of individual amide proton exchange rates by two-dimensional correlated 1H NMR spectroscopy (COSY) showed that the exchange was slowest for some hydrogen bonded amide groups in an alpha-helix. This contrasts with all other proteins which were so far studied in detail, where the slowest exchange rates were observed for hydrogen bonded amide protons in antiparallel beta-sheets.
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50
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Bennett WS, Huber R. Structural and functional aspects of domain motions in proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1984; 15:291-384. [PMID: 6325088 DOI: 10.3109/10409238409117796] [Citation(s) in RCA: 206] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Three distinct categories of large-scale flexibility in proteins have been documented by single-crystal X-ray diffraction studies: the relatively free movement of essentially rigid globular domains that are connected by a flexible segment of polypeptide, the reorientation of essentially rigid domains among a few distinct conformations, and the concerted transition of a contiguous region of the surface of a protein from a disordered state to an ordered state. In a number of examples, well-defined functions can be assigned to these large-scale structural changes. The occurrence of such motions in proteins of known structure is reviewed, and the best-studied examples are discussed in detail to allow a critical evaluation of the methods used to identify and study these motions.
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