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Singh R, Manna S, Nandanwar H, Purohit R. Bioactives from medicinal herb against bedaquiline resistant tuberculosis: removing the dark clouds from the horizon. Microbes Infect 2024; 26:105279. [PMID: 38128751 DOI: 10.1016/j.micinf.2023.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Tuberculosis is a contagious bacterial ailment that primarily affects the lungs and is brought on by the bacterium Mycobacterium tuberculosis (MTB). An antimycobacterial medication called bedaquiline (BQ) is specified to treat multidrug-resistant tuberculosis (MDR-TB). Despite its contemporary use in clinical practice, the mutations (D32 A/G/N/V/P) constrain the potential of BQ by causing transitions in the structural conformation of the atpE subunit-c after binding. In this study, we have taken the benzylisoquinoline alkaloids from thalictrum foliolosum due to its antimicrobial activity reported in prior literature. We used an efficient and optimized structure-based strategy to examine the wild type (WT) and mutated protein upon molecule binding. Our results emphasize the drastic decline in BQ binding affinity of mutant and WT atpE subunit-c complexes compared to thalirugidine (top hit) from thalictrum foliolosum. The decrease in BQ binding free energy is due to electrostatic energy because nearly every atom in a macromolecule harbors a partial charge, and molecules taking part in molecular recognition will interact electrostatically. Similarly, the high potential mean force of thalirugidine than BQ in WT and mutant complexes demonstrated the remarkable ability to eradicate mycobacteria efficiently. Furthermore, the Alamar blue cell viability and ATP determination assay were performed to validate the computational outcomes in search of novel antimycobacterial. Upon closer examination of the ATP determination assay, it became apparent that both BQ and thalirugidine showed similar reductions in ATP levels at their respective MICs, presenting a potential common mechanism of action.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Souvik Manna
- CSIR-Institute of Microbial Technology, Sector-39, Chandigarh, 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemraj Nandanwar
- CSIR-Institute of Microbial Technology, Sector-39, Chandigarh, 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023; 127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/25/2022] [Indexed: 01/15/2023]
Abstract
Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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Affiliation(s)
- Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06129 Halle (Saale), Germany
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3
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Martin BT, Malmstrom RD, Amaro RE, Wüthrich K. OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring-Flip Frequencies Determined by Integrated Use of 1 H NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2020; 22:565-570. [PMID: 32975902 DOI: 10.1002/cbic.202000517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/18/2020] [Indexed: 11/12/2022]
Abstract
The 55-residue OCRE domains of the splicing factors RBM5 and RBM10 contain 15 tyrosines in compact, globular folds. At 25 °C, all 15 tyrosines show symmetric 1 H NMR spectra, with averaged signals for the pairs of δ- and ϵ-ring hydrogens. At 4 °C, two tyrosines were identified as showing 1 H NMR line-broadening due to lowered frequency of the ring-flipping. For the other 13 tyrosine rings, it was not evident, from the 1 H NMR data alone, whether they were either all flipping at high frequencies, or whether slowed flipping went undetected due to small chemical-shift differences between pairs of exchanging ring hydrogen atoms. Here, we integrate 1 H NMR spectroscopy and molecular dynamics (MD) simulations to determine the tyrosine ring-flip frequencies. In the RBM10-OCRE domain, we found that, for 11 of the 15 tyrosines, these frequencies are in the range 2.0×106 to 1.3×108 s-1 , and we established an upper limit of <1.0×106 s-1 for the remaining four residues. The experimental data and the MD simulation are mutually supportive, and their combined use extends the analysis of aromatic ring-flip events beyond the limitations of routine 1 H NMR line-shape analysis into the nanosecond frequency range.
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Affiliation(s)
- Bryan T Martin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, MB 44, La Jolla, CA 92037, USA.,Present address: Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert D Malmstrom
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA.,5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, MB 44, La Jolla, CA 92037, USA.,Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
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4
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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5
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Dimova M, Devedjiev YD. Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase. IUCRJ 2018; 5:130-140. [PMID: 29765602 PMCID: PMC5947717 DOI: 10.1107/s2052252517017833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 12/13/2017] [Indexed: 05/03/2023]
Abstract
Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.
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Affiliation(s)
- Margarita Dimova
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
| | - Yancho D. Devedjiev
- Department of Anesthesiology, University of Virginia, 1215 Lee Street, Charlottesville, VA 22908, USA
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6
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Vugmeyster L, Ostrovsky D, Villafranca T, Sharp J, Xu W, Lipton AS, Hoatson GL, Vold RL. Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR. J Phys Chem B 2015; 119:14892-904. [PMID: 26529128 PMCID: PMC4970646 DOI: 10.1021/acs.jpcb.5b09299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298-80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is nonexponential at all temperatures with the extent of nonexponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al. J. Phys. Chem. B 2013, 117, 6129-6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The crossover temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions.
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Affiliation(s)
| | | | | | - Janelle Sharp
- University of Alaska Anchorage, Anchorage, Alaska, 99508
| | - Wei Xu
- College of William and Mary, Williamsburg, Virginia, 23187
| | - Andrew S. Lipton
- Pacific Northwest National Laboratory, Richland, Washington, 99354
| | | | - Robert L. Vold
- College of William and Mary, Williamsburg, Virginia, 23187
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7
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Weininger U, Modig K, Akke M. Ring Flips Revisited: 13C Relaxation Dispersion Measurements of Aromatic Side Chain Dynamics and Activation Barriers in Basic Pancreatic Trypsin Inhibitor. Biochemistry 2014; 53:4519-25. [DOI: 10.1021/bi500462k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ulrich Weininger
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Kristofer Modig
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mikael Akke
- Department of Biophysical
Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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8
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Huber R. “Wie ich zur Proteaseforschung kam oder, richtiger gesagt, wie die Proteaseforschung zu mir kam”. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Huber R. "How I chose research on proteases or, more correctly, how it chose me". Angew Chem Int Ed Engl 2012. [PMID: 23208749 DOI: 10.1002/anie.201205629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert Huber
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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10
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Abstract
Mean packing densities in protein interiors are comparable to those of most organic solids but the variations between small regions may be substantial. Packing defects may be related to allowed structural fluctuations. Molecular surface areas can be correlated with free energies of transfer between different solvents. The proportionality factor will depend, in general, on the nature of the solute and both the solvents. The changes in solvent-protein interfacial area on chain folding are large and the implied changes in free energy from this solvent-squeezing effect are correspondingly large. The strong tendency to minimize surface area is reflected in the globular shape of most protein molecules or domains in larger structures. The formation of isolated units of secondary structure from an extended chain represents about one half of the eventual total area change. The tendencies of amino acids to form beta-sheets correlate well with the rank-ordered list based on non-polar area change for each residue type. The calculated area changes for helix and sheet formation are not identical in rank order. The rank-ordered list for alpha-helix formation correlates satisfactorily with the probability list prepared from actual structures if glutamic acid and tyrosine are removed. What special characteristics unrelated to surface area these two amino acids might have is not clear. Tertiary structure formation from preformed secondary structural units can be rank ordered on area change and possible nucleation sites can be identified. A prediction scheme for helix-helix interactions is proposed. The hydrophobic force begins to be felt when two helices are about 0.6 nm (6 A) from their final contact positions. Interfacial surface tension is a logical parameter to relate free energy and solvent contact area, but this macroscopic parameter must be used with great caution. It is suggested that water in the deep grooves, characteristic of the active sites of many enzymes, may have a substantially higher fugacity than bulk water as indicated, at least qualitatively, by the Kelvin equation based on surface curvature. Such water would be more easily displaced than its plane surface counterpart and could contribute significantly to ligand-binding energy. This factor would be in addition to the usual solvent entropic effects associated with surface area reduction on association.
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11
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Blake CC, Grace DE, Johnson LN, Perkins SJ, Phillips DC, Cassels R, Dobson CM, Poulsen FM, Williams RJ. Physical and chemical properties of lysozyme. CIBA FOUNDATION SYMPOSIUM 2008:137-85. [PMID: 252451 DOI: 10.1002/9780470720424.ch10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The conformations of lysozyme in crystals and in aqueous solution are discussed and it is shown that the basic conformation is similar in the two states. Certain parts of the molecule have mobility. The reactions of lysozyme with protons, metal ions and some organic reagents are examined in the light of the conformations and their dynamics. The reactions considered are mainly those of tyrosyl, tryptophyl and carboxylate residues. The reactivity data are used in a discussion of the energy states of the reacting side-chains. In particular the reactivity of Glu-35 and its interaction with Trp-108 lead to suggestions for some new aspects in the hypothesis for the mechanism of action of lysozyme. In most respects the X-ray crystal diffraction and the nuclear magnetic resonance solution studies are in accord and complementary.
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12
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Wüthrich K. Six years of protein structure determination by NMR spectroscopy: what have we learned? CIBA FOUNDATION SYMPOSIUM 2007; 161:136-45; discussion 145-9. [PMID: 1726080 DOI: 10.1002/9780470514146.ch9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy in solution is a second technique, in addition to X-ray diffraction in single crystals, for the determination of three-dimensional protein structures at atomic resolution. Structures of proteins derived by NMR have now been with us for six years, and here I entertain the following question: what information have we gained that would not be available if X-ray crystallography were still the only method for protein structure determination? Answers include that NMR structures are available of proteins that have not been crystallized, that the two techniques afford different insights into internal mobility of proteins, and that one gets different views of protein hydration and hence the molecular surface when using NMR spectroscopy or X-ray diffraction.
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Affiliation(s)
- K Wüthrich
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
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13
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Hattori M, Li H, Yamada H, Akasaka K, Hengstenberg W, Gronwald W, Kalbitzer HR. Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips. Protein Sci 2005; 13:3104-14. [PMID: 15557257 PMCID: PMC2287304 DOI: 10.1110/ps.04877104] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88-residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on-line cell high-pressure nuclear magnetic resonance technique in the pressure range from 3 MPa to 200 MPa and in the temperature range from 257 K to 313 K. The ring of Tyr6 is buried sandwiched between a beta-sheet and alpha-helices (the water-accessible area is less than 0.26 nm2), its hydroxyl proton being involved in an internal hydrogen bond. The ring flip rates 10(1)-10(5) s(-1) were determined from the line shape analysis of H(delta1, delta2) and H(epsilon1,epsilon2) of Tyr6, giving an activation volume DeltaV++ of 0.044 +/- 0.008 nm3 (27 mL mol(-1)), an activation enthalpy DeltaH++ of 89 +/- 10 kJ mol(-1), and an activation entropy DeltaS++ of 16 +/- 2 JK(-1) mol(-1). The DeltaV++) and DeltaH++ values for HPr found previously for Tyr and Phe ring flips of BPTI and cytochrome c fall within the range of DeltaV(double dagger) of 28 to 51 mL mol(-1) and DeltaH++ of 71 to 155 kJ mol(-1). The fairly common DeltaV++ and DeltaH++ values are considered to represent the extra space or cavity required for the ring flip and the extra energy required to create a cavity, respectively, in the core part of a globular protein. Nearly complete cold denaturation was found to take place at 200 MPa and 257 K independently from the ring reorientation process.
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Affiliation(s)
- Mineyuki Hattori
- Department of Molecular Science, Graduate School of Science and Technology, Kobe University, Japan
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14
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Karplus M, McCammon J. Pressure dependence of aromatic ring rotations in proteins: a collisional interpretation. FEBS Lett 2001. [DOI: 10.1016/0014-5793(81)80881-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Abstract
Interactions between biological macromolecules have characteristic values of affinity and specificity that are set according to the biological function that is served by the interaction in the organism. Here we examine the molecular mechanisms that are used to achieve the required values of affinity and specificity in various biological systems.
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Affiliation(s)
- D Szwajkajzer
- Princeton University, Department of Chemistry, NJ 08544, USA
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16
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Polshakov VI, Birdsall B, Feeney J. Characterization of rates of ring-flipping in trimethoprim in its ternary complexes with Lactobacillus casei dihydrofolate reductase and coenzyme analogues. Biochemistry 1999; 38:15962-9. [PMID: 10625463 DOI: 10.1021/bi9915263] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR measurements have been used to investigate rates of ring-flipping and the activation parameters for the trimethoxybenzyl ring of the antibacterial drug trimethoprim (TMP) bound to Lactobacillus casei dihydrofolate reductase (DHFR) for a series of ternary complexes formed with analogues of the coenzyme NADPH. Rates were obtained at several temperatures from line shape analyses ((13)C-edited HSQC (1)H spectra) and transfer of magnetization measurements (zz-HSQC) on complexes containing 3'-O-[(13)C]trimethoprim. Examination of the structures of the complexes indicates that ring-flipping can only be achieved following major conformational changes and transient fluctuations of the protein and coenzyme structure around the trimethoxybenzyl ring. There is no simple correlation between rates of ring-flipping and binding constants. The presence of the coenzyme nicotinamide ring (in either its reduced or its oxidized forms) in the binding site close to the trimethoxybenzyl ring moiety is the major factor reducing the ring-flipping on coenzyme binding. Thus, the ternary complex with NADPH shows the largest reduction in the rate of ring-flipping (11 +/- 3 s(-)(1) at 298 K) as compared with the binary complex (793 +/- 80 s(-)(1) at 298 K). Complexes with NADPH analogues that either have no nicotinamide ring or are known to have their nicotinamide rings removed from the binding site show the smallest reductions. For the DHFR.TMP.NADP(+) complex where there are two conformations present, very different rates of ring-flipping were observed for the two forms. The activation parameters (DeltaH() and DeltaS()) for the ring-flipping in all the complexes are discussed in terms of the protein-ligand interactions and the possible constraints on the pathway through the transition state.
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Affiliation(s)
- V I Polshakov
- Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, U.K., and Center for Drug Chemistry, Moscow 119815, Russia
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19
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Dobson CM, Karplus M. Internal motion of proteins: nuclear magnetic resonance measurements and dynamic simulations. Methods Enzymol 1986; 131:362-89. [PMID: 3773766 DOI: 10.1016/0076-6879(86)31049-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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20
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Chapter 1 Nuclear magnetic resonance spectroscopy in biochemistry. NEW COMPREHENSIVE BIOCHEMISTRY 1985. [DOI: 10.1016/s0167-7306(08)60560-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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21
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Clore GM, Gronenborn AM, Birdsall B, Feeney J, Roberts GC. 19F-n.m.r. studies of 3',5'-difluoromethotrexate binding to Lactobacillus casei dihydrofolate reductase. Molecular motion and coenzyme-induced conformational changes. Biochem J 1984; 217:659-66. [PMID: 6424648 PMCID: PMC1153266 DOI: 10.1042/bj2170659] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
19F-n.m.r. spectroscopy was used to study the binding of 3',5'-difluoromethotrexate to dihydrofolate reductase (tetrahydrofolate dehydrogenase) from Lactobacillus casei. The benzoyl ring of the bound difluoromethotrexate was found to 'flip' about its symmetry axis, and the rate (7.3 X 10(3) s-1 at 298 K) and activation parameters for this process were determined by lineshape analysis of the 19F-n.m.r. spectrum at a series of temperatures in the range 273-308 K. The contributions to the barrier for this process are discussed. Addition of NADP+ or NADPH to form the enzyme-difluoromethotrexate-coenzyme ternary complex led to an increase in the rate of benzoyl ring flipping by a factor of 2.6-2.8-fold, and to substantial changes in the 19F-n.m.r. chemical shifts. The possible nature of the coenzyme-induced conformational changes responsible for these effects is discussed.
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22
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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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23
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Englander SW, Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 1983; 16:521-655. [PMID: 6204354 DOI: 10.1017/s0033583500005217] [Citation(s) in RCA: 965] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Though the structures presented in crystallographic models of macromolecules appear to possess rock-like solidity, real proteins and nucleic acids are not particularly rigid. Most structural work to date has centred upon the native state of macromolecules, the most probable macromolecular form. But the native state of a molecule is merely its most abundant form, certainly not its only form. Thermodynamics requires that all other possible structural forms, however improbable, must also exist, albeit with representation corresponding to the factor exp( —Gi/RT) for each state of free energyGi(see Moelwyn-Hughes, 1961), and one appreciates that each molecule within a population of molecules will in time explore the vast ensemble ofpossiblestructural states.
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24
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Wagner G. Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes. Q Rev Biophys 1983; 16:1-57. [PMID: 6878622 DOI: 10.1017/s0033583500004911] [Citation(s) in RCA: 191] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed. This demonstration of a manifold of spatial fluctuations in a small protein provides an impression on the kind of fluctuations which have to be expected for larger proteins. When studying protein reactions one should therefore consider the presence of a large number of different, transiently formed, spatial structures available for the partner in the reaction, which may pick out only that structure which will optimally perform a particular reaction with the highest efficiency.
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25
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Northrup SH, Pear MR, Lee CY, McCammon JA, Karplus M. Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci U S A 1982; 79:4035-9. [PMID: 6955788 PMCID: PMC346571 DOI: 10.1073/pnas.79.13.4035] [Citation(s) in RCA: 161] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A method is described for calculating the reaction rate in globular proteins of activated processes such as ligand binding or enzymatic catalysis. The method is based on the determination of the probability that the system is in the transition state and of the magnitude of the reactive flux for transition-state systems. An "umbrella sampling" simulation procedure is outlined for evaluating the transition-state probability. The reactive flux is obtained from an approach described previously for calculating the dynamics of transition-state trajectories. An application to the rotational isomerization of an aromatic ring in the bovine pancreatic trypsin inhibitor is presented. The results demonstrate the feasibility of calculating rate constants for reactions in proteins and point to the importance of solvent effects for reactions that occur near the protein surface.
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26
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Billeter M, Braun W, Wüthrich K. Sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. Computation of sterically allowed proton-proton distances and statistical analysis of proton-proton distances in single crystal protein conformations. J Mol Biol 1982; 155:321-46. [PMID: 7077676 DOI: 10.1016/0022-2836(82)90008-0] [Citation(s) in RCA: 416] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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27
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Nagayama K, Wüthrich K. Structural interpretation of vicinal proton-proton coupling constants 3JH alpha H beta in the basic pancreatic trypsin inhibitor measured by two-dimensional J-resolved NMR spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 115:653-7. [PMID: 6165586 DOI: 10.1111/j.1432-1033.1981.tb06252.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Two-dimensional J-resolved 1H NMR spectroscopy was used to measure the vicinal spin-spin coupling constants 3JH alpha H beta for numerous, previously individually assigned amino acid residues in the basic pancreatic trypsin inhibitor at various temperatures between 30 and 85 degrees JC. An analysis of this data is proposed which enables one to compare the spatial arrangements of individual amino acid side chains in solution and in single crystals of the protein, and which also provides information on the mobility of the side chains in the solution conformation. As a rule, the amino acid side chains in the interior of the protein were found to be locked into unique spatial orientations, with the mobility restricted to rapid rotational fluctuations about this unique value for the dihedral angle chi 1. In most, but not all, instances the data for the interior amino acids indicate identical average conformations for the amino acid side chains in single crystals and in solution. For residues on the protein surface structural rearrangements between crystal and solution appear to be common, and the mobility in the solution conformation may include rapid averaging between two or several distinct, preferentially populated values of chi 1, analogous to the gauche-trans-gauche isomerization in isolated amino acids.
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28
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Karplus M, McCammon JA. The internal dynamics of globular proteins. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 9:293-349. [PMID: 7009056 DOI: 10.3109/10409238109105437] [Citation(s) in RCA: 422] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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29
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Wüthrich K, Wagner G, Richarz R, Braun W. Correlations between internal mobility and stability of globular proteins. Biophys J 1980; 32:549-60. [PMID: 7248460 PMCID: PMC1327351 DOI: 10.1016/s0006-3495(80)84989-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The recent work is surveyed which leads to the suggestions that the conformation of globular proteins in solution corresponds to a dynamic ensemble of rapidly interconverting spatial structures, that clusters of hydrophobic amino acid side chains have an important role in the architecture of protein molecules, and that mechanistic aspects of protein denaturation can be correlated with internal mobility seen in the native conformation. These conclusions resulted originally from high resolution 1H nuclear magnetic resonance (NMR) studies of aromatic ring mobility, exchange of interior amide protons and thermal denaturation of the basic pancreatic trypsin inhibitor and a group of related proteins. Various new approaches to further characterize proteins in solution have now been taken and preliminary data are presented. These include computer graphics to outline hydrophobic clusters in globular protein structures, high resolution 1H-NMR experiments at variable hydrostatic pressure and 13C-NMR relaxation measurements. At the present early stage of these new investigations it appears that the hydrophobic cluster model for globular proteins is compatible with the data obtained.
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30
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Karplus M, Gelin BR, McCammon JA. Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI. Biophys J 1980; 32:603-18. [PMID: 7248464 PMCID: PMC1327359 DOI: 10.1016/s0006-3495(80)84993-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Theoretical approaches to the internal dynamics of proteins are outlined and illustrated by application to the aromatic sidechain motions of tyrosines in the bovine pancreatic trypsin inhibitor. High frequency torsional oscillations are obtained from a molecular dynamics simulation, while the longer time ring rotations are analyzed by use of adiabatic energy minimization and special transition-state trajectory techniques.
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31
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32
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33
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Wagner G. Activation volumes for the rotational motion of interior aromatic rings in globular proteins determined by high resolution 1H NMR at variable pressure. FEBS Lett 1980; 112:280-4. [PMID: 6154600 DOI: 10.1016/0014-5793(80)80198-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Perkins SJ, Wüthrich K. Conformational transition from trypsinogen to trypsin. 1H nuclear magnetic resonance at 360 MHz and ring current calculations. J Mol Biol 1980; 138:43-64. [PMID: 7411606 DOI: 10.1016/s0022-2836(80)80004-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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35
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Moore GR, Williams RJ. Nuclear-magnetic-resonance studies of ferrocytochrome c. pH and temperature dependence. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 103:513-21. [PMID: 6244160 DOI: 10.1111/j.1432-1033.1980.tb05975.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The pH dependence and the temperature dependence of the nuclear magnetic resonance spectrum of horse ferrocytochrome c are described. This protein is very stable; it maintains an ordered structure over the pH range 4 to 12 at 25 degrees C and over the temperature range 4 degrees C to 97 degrees C at pH 7.0. The dynamic characteristics of the conformation of ferrocytochrome c were investigated. Particular emphasis was laid on the aromatic resonances and resonances of methyl groups shifted far upfield. Tyr-48 and Phe-46 were found to be relatively immobile whilst a region of the protein close to Ile-57 was found to be relatively flexible.
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36
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37
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Wüthrich K, Wagner G. Nuclear magnetic resonance of labile protons in the basic pancreatic trypsin inhibitor. J Mol Biol 1979; 130:1-18. [PMID: 38342 DOI: 10.1016/0022-2836(79)90548-5] [Citation(s) in RCA: 164] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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38
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Gelin BR, Karplus M. Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. Biochemistry 1979; 18:1256-68. [PMID: 427111 DOI: 10.1021/bi00574a022] [Citation(s) in RCA: 257] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Side-chain torsional potentials in the bovine pancreatic trypsin inhibitor are calculated from empirical energy functions by use of the known X-ray structure of the protein and the rigid-geometry mapping technique. The potentials are analyzed to determine the roles and relative importance of contributions from the dipeptide backbone, the protein, and the crystalline environment of solvent and other protein molecules. The structural characteristics of the side chains determine two major patterns of energy surfaces, E(X1,X2): a gamma-branched pattern and a pattern for longer, straight side chains (Arg, Lys, Glu, and Met). Most of the dipeptide potential curves and surfaces have a local minimum corresponding to the side-chain torsional angles in the X-ray structure. Addition of the protein forces sharpens and/or selects from these minima, providing very good agreement with the experimental conformation for most side chains at the surface or in the core of the protein. Inclusion of the crystalline environment produces still better results, especially for the side chains extending away from the protein. The results are discussed in terms of the details of the interactions due to the surrounding, calculated solvent-accessibility figures and the temperature factors derived from the crystallographic refinement of the pancreatic trypsin inhibitor.
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39
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Wagner G, Tschesche H, Wüthrich K. The influence of localized chemical modifications of the basic pancreatic trypsin inhibitor on static and dynamic aspects of the molecular conformation in solution. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 95:239-48. [PMID: 313337 DOI: 10.1111/j.1432-1033.1979.tb12959.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Dubs A, Wagner G, Wüthrich K. Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 577:177-94. [PMID: 311660 DOI: 10.1016/0005-2795(79)90020-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Studies of proton-proton nuclear Overhauser effects were used to obtain individual assignments of 17 amide proton resonances in the 360 MHz proton nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor. First, optimizing the conditions for obtaining selective nuclear Overhauser effects in the presence of spin diffusion in macromolecules is discussed. Truncated driven nuclear Overhauser experiments were used to assing the amide proton resonances of the beta-sheet in the inhibitor. It is suggested that these techniques could serve quite generally to obtain individual resonance assignments in beta-sheet secondary structures of proteins. Combination of nuclear Overhauser studies with spin decoupling further resulted in individual assignments of the gamma-methyl resonances of the two isoleucines and numerous Calpha and Cbeta protons.
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41
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Perkins SJ, Wüthrich K. Ring current effects in the conformation dependent NMR chemical shifts of aliphatic protons in the basic pancreatic trypsin inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 576:409-23. [PMID: 427198 DOI: 10.1016/0005-2795(79)90416-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Previously, a highly refined crystal structure and energy refined atomic coordinates were obtained for the basic pancreatic trypsin inhibitor, as well as numerous individual resonance assignments in the 1H NMR spectrum. These data were now used to investigate the contributions from the local ring current fields of the aromatic rings to the overall conformation dependent chemical shifts in this globular protein. A program was written which allowed the consideration of certain aspects of internal mobility of the protein, and the different commonly used ring current equa tions were compared. These studies indicate that ring current shifts are the dominant contribution to the observed conformation dependent chemical shifts of the peripheral aliphatic side chain protons. On the other hand, it appears that ring current shifts do not make dominant contributions to the conformation dependent shifts of the backbone alpha- and amide protons or the aromatic protons in the inhibitor. On the basis of the empirical calibration with the peripheral aliphatic side chain protons, the Johnson-Bovey ring current equation was selected for an analysis of the ring geometries of two prolines in the inhibitor.
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42
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43
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Creighton TE. Experimental studies of protein folding and unfolding. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1979; 33:231-97. [PMID: 358273 DOI: 10.1016/0079-6107(79)90030-0] [Citation(s) in RCA: 380] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Perkins SJ, Wüthrich K. Structural interpretation of lanthanide binding to the basic pancreatic trypsin inhibitor by 1H NMR at 360 MHz. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 536:406-20. [PMID: 30488 DOI: 10.1016/0005-2795(78)90498-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The weak binding of lanthanides to the five carboxyl groups of the basic pancreatic trypsin inhibitor (hereafter termed "the inhibitor"), has been investigated in detail using high resolution 1H NMR at 360 MHz. Lanthanides bind to the C-terminus with an apparent binding constant of 30 M-1, and thus competitively inhibit the formation of a salt-bridge between the C-terminus and the N-terminus, Lanthanides bind also to the side chain carboxyl groups of Asp 3, Glu 7, Glu 49 and Asp 50, with binding constants of 10--30 M-1. With the use of lanthanides individual resonance assignments for Phe 4 and Phe 45 were obtained in the 1H NMR spectrum of the inhibitor, and for several spin systems previous identifications were independently confirmed. The present experiments also provide a nice illustration for the use of shift reagents to improve the resolution in 1H NMR spectra of proteins. The exchange broadening for Tyr 35 and Phe 45 over the temperature range 4--72 degrees C could thus be observed for almost all the components of these aromatic spin systems and new details on the dynamic properties were obtained also for other aromatic residues.
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45
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46
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Wagner G, Wüthrich K. Dynamic model of globular protein conformations based on NMR studies in solution. Nature 1978; 275:247-8. [PMID: 692702 DOI: 10.1038/275247a0] [Citation(s) in RCA: 85] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Wagner G, Wüthrich K, Tschesche H. A 1H nuclear-magnetic-resonance study of the solution conformation of the isoinhibitor K from Helix pomatia. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:367-77. [PMID: 710398 DOI: 10.1111/j.1432-1033.1978.tb12538.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The isoinhibitor K from Helix pomatia was investigated by high-resolution 1H nuclear magnetic resonance at 360 MHZ. Detailed studies of the labile protons and the resonances of the aromatic residues indicated extensive homologies between the spatial structures of the snail inhibitor, the basic pancreatic trypsin inhibitor (Kunitz) from bovine tissue and the cos colostrum trypsin inhibitor. Comparison of these three homologous inhibitors indicated that the overall flexibility of the globular protein conformation is reduced and its stability with respect to thermal denaturation raised when the content of amino acids with charged side chains is increased. It is suggested that this relation between amino acid composition and stability of the globular solution structure might be valid also for other classes of homologous proteins.
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48
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Hilton BD, Woodward CK. Nuclear magnetic resonance measurement of hydrogen exchange kinetics of single protons in basic pancreatic trypsin inhibitor. Biochemistry 1978; 17:3325-32. [PMID: 28747 DOI: 10.1021/bi00609a024] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Creighton TE, Kalef E, Arnon R. Immunochemical analysis of the conformational properties of intermediates trapped in the folding and unfolding of bovine pancreatic trypsin inhibitor. J Mol Biol 1978; 123:129-47. [PMID: 98640 DOI: 10.1016/0022-2836(78)90317-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Wüthrich K, Wagner G, Richarz R, Perkins SJ. Individual assignments of the methyl resonances in the 1H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor. Biochemistry 1978; 17:2253-63. [PMID: 307961 DOI: 10.1021/bi00605a001] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In earlier work the resonances of the 20 methyl groups in the basic pancreatic trypsin inhibitor (BPTI) had been identified in the 360-MHz 1H nuclear magnetic resonance (NMR) spectra and most of the methyl lines had from spin-decoupling experiments been assigned to the different types of amino acid residues. The assignments to the different amino acid types were now completed by studies of the saturation transfer between the denatured and the globular forms of the inhibitor and by spin-decoupling experiments in nuclear Overhauser enhancement (NOE) difference spectra. These distinguished between the methyl resonances of Ala and Thr. Furthermore, for most of the methyl resonances, individual assignments to specific residues in the amino acid sequence were obtained from measurements of intramolecular proton-proton NOE's, use of lanthanide NMR shift and relaxation probes, and comparative studies of various chemically modified forms of BPTI. These data provide the basis for individual assignments of the methyl 13C NMR lines in BPTI and for detailed investigations of the relations between the spatial structure of the protein and the chemical shifts of the methyl groups. The methyl groups in BPTI are of particular interest since they are located almost exclusively on the surface of the protein and thus represent potential natural NMR probes for studies of the protein-protein interactions in the complexes formed between BPTI and a variety of proteases.
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