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Boelens R, Ivanov K, Matysik J. Introduction to a special issue of Magnetic Resonance in honour of Robert Kaptein at the occasion of his 80th birthday. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:465-474. [PMID: 37904778 PMCID: PMC10539797 DOI: 10.5194/mr-2-465-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 11/01/2023]
Abstract
This publication, in honour of Robert Kaptein's 80th birthday, contains contributions from colleagues, many of whom have worked with him, and others who admire his work and have been stimulated by his research. The contributions show current research in biomolecular NMR, spin hyperpolarisation and spin chemistry, including CIDNP (chemically induced dynamic nuclear polarisation), topics to which he has contributed enormously. His proposal of the radical pair mechanism was the birth of the field of spin chemistry, and the laser CIDNP NMR experiment on a protein was a major breakthrough in hyperpolarisation research. He set milestones for biomolecular NMR by developing computational methods for protein structure determination, including restrained molecular dynamics and 3D NMR methodology. With a lac repressor headpiece, he determined one of the first protein structures determined by NMR. His studies of the lac repressor provided the first examples of detailed studies of protein nucleic acid complexes by NMR. This deepened our understanding of protein DNA recognition and led to a molecular model for protein sliding along the DNA. Furthermore, he played a leading role in establishing the cluster of NMR large-scale facilities in Europe. This editorial gives an introduction to the publication and is followed by a biography describing his contributions to magnetic resonance.
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Affiliation(s)
- Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Konstantin Ivanov
- International Tomography Center, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University,
Novosibirsk 630090, Russia
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04189 Leipzig, Germany
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De Vlieg J, Boelens R, Scheek RM, Kaptein R, van Gunsteren WF. Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: ALacRepressor Headpiece Structure Based on Information on J-coupling and from Presence and Absence of NOE's. Isr J Chem 2013. [DOI: 10.1002/ijch.198600027] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bock JL. Recent developments in biochemical nuclear magnetic resonance spectroscopy. METHODS OF BIOCHEMICAL ANALYSIS 2006; 31:259-315. [PMID: 3894882 DOI: 10.1002/9780470110522.ch6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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van Geerestein-Ujah EC, Slijper M, Boelens R, Kaptein R. Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece. JOURNAL OF BIOMOLECULAR NMR 1995; 6:67-78. [PMID: 7663143 DOI: 10.1007/bf00417493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the 15N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.
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STRUCTURE DETERMINATION OF BIOLOGICAL MACROMLECULES BY NMR IN SOLUTION: IMPACT IN BIOMEDICAL RESEARCH. Eur J Med Chem 1995. [DOI: 10.1016/s0223-5234(23)00115-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Lancelot G, Gervais A, Maurizot JC. Two-dimensional 1H, 15N NMR investigation of uniformly 15N-labeled lac repressor headpiece. J Biomol Struct Dyn 1992; 9:921-33. [PMID: 1524707 DOI: 10.1080/07391102.1992.10507967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
15N uniformly labeled lac repressor and lac repressor headpiece were prepared. 15N NMR spectra of lac repressor were shown resolution inadequate for detailed study while the data showed that the 15N labeled N-terminal part of the protein is quite suitable for this type of study allowing future investigation of the specific interaction of the lac repressor headpiece with the lac operator. We report here the total assignment of proton 1H and nitrogen 15NH backbone resonances of this headpiece in the free state. Assignments of the 15N resonances of the protein were obtained in a sequential manner using heteronuclear multiple quantum coherence (HMQC), relayed HMQC nuclear Overhauser and relayed HMQC-HOHAHA spectroscopy. More than 80 per cent of residues were assigned by their 15NH(i)-N1H(i + 1) and 15NH(i)-N1H(i - 1) connectivities. Values of the 3JNH alpha splitting for 39 of the 51 residues of the headpiece were extracted from HMQC and HMQC-J. The observed 15NH(i)-C beta H cross peaks and the 3JNH alpha coupling constants values are in agreement with the three alpha-helices previously described [Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., van Gunsteren, W.F. and Kaptein, R., Biochimie 67, 707 (1985)]. The 3JNH alpha coupling constants can be now used for a more confident determination of the lac repressor headpiece. From these values it is shown that the geometry of the ends of the second and third alpha-helices exhibit deviation from the canonical alpha-helix structure. On the basis of NOEs and 3JNH alpha values, the geometry of the turn of the helix-turn-helix motif is discussed.
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Affiliation(s)
- G Lancelot
- Centre de Biophysique Moleculaire, CNRS, Orleans, France
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8
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The role of the N terminus in Tet repressor for tet operator binding determined by a mutational analysis. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)46038-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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9
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Shin JA, Ebright RH, Dervan PB. Orientation of the Lac repressor DNA binding domain in complex with the left lac operator half site characterized by affinity cleaving. Nucleic Acids Res 1991; 19:5233-6. [PMID: 1923807 PMCID: PMC328881 DOI: 10.1093/nar/19.19.5233] [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: 12/29/2022] Open
Abstract
Lac repressor (LacR) is a helix-turn-helix motif sequence-specific DNA binding protein. Based on proton NMR spectroscopic investigations, Kaptein and co-workers have proposed that the helix-turn-helix motif of LacR binds to DNA in an orientation opposite to that of the helix-turn-helix motifs of lambda repressor, lambda cro, 434 repressor, 434 cro, and CAP [Boelens, R., Scheek, R., van Boom, J. and Kaptein, R., J. Mol. Biol. 193, 1987, 213-216]. In the present work, we have determined the orientation of the helix-turn-helix motif of LacR in the LacR-DNA complex by the affinity cleaving method. The DNA cleaving moiety EDTA.Fe was attached to the N-terminus of a 56-residue synthetic protein corresponding to the DNA binding domain of LacR. We have formed the complex between the modified protein and the left DNA half site for LacR. The locations of the resulting DNA cleavage positions relative to the left DNA half site provide strong support for the proposal of Kaptein and co-workers.
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Affiliation(s)
- J A Shin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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10
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Affiliation(s)
- P S Freemont
- Protein Structure Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, U.K
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11
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Wüthrich K, Spitzfaden C, Memmert K, Widmer H, Wider G. Protein secondary structure determination by NMR. Application with recombinant human cyclophilin. FEBS Lett 1991; 285:237-47. [PMID: 1855591 DOI: 10.1016/0014-5793(91)80808-g] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
It is a unique trait of the NMR method for protein structure determination that a description of the polypeptide secondary structure can be obtained at an early stage and quite independently of the complete structure calculation. In this paper the procedures used for secondary structure determination are reviewed and placed in perspective relative to the other steps in a complete three-dimensional structure determination. As an illustration the identification of the regular secondary structure elements in human cyclophilin is described.
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Affiliation(s)
- K Wüthrich
- Institut für Molekularbiologie und Biophysik, ETH Hönggerberg, Zürich, Switzerland
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12
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Kisters-Woike B, Lehming N, Sartorius J, von Wilcken-Bergmann B, Müller-Hill B. A model of the lac repressor-operator complex based on physical and genetic data. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 198:411-9. [PMID: 2040302 DOI: 10.1111/j.1432-1033.1991.tb16030.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Computer graphics were used to build a molecular model of the complex of Lac repressor and lac operator. The model is based (a) on the NMR data of the Kaptein group [Boelens, R., Lamerichs, R. M. J. N., Rullmann, J. A. C., van Boom, J. H. & Kaptein, R. (1988) Protein Sequence Data Anal. 1, 487-498] and (b) on our genetic and biochemical data including specificity changes [Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1990) EMBO J. 9, 615-621]. Effects of amino acid exchanges in the recognition helix could be predicted by the model and were subsequently tested and confirmed by genetic experiments. Comparison of the modelled lac complex with the known crystallographic structures of several helix-turn-helix DNA complexes reveals striking similarities and suggests rules which govern the recognition between particular amino acid side chains and particular base pairs in these systems.
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Affiliation(s)
- B Kisters-Woike
- Institut für Genetik, Universität zu Köln, Federal Republic of Germany
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14
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Sunnarborg A, Klumpp D, Chung T, LaPorte DC. Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. J Bacteriol 1990; 172:2642-9. [PMID: 2185227 PMCID: PMC208908 DOI: 10.1128/jb.172.5.2642-2649.1990] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In Escherichia coli, expression of the glyoxylate bypass operon appears to be controlled, in part, by the product of iclR+. Mutations in iclR have been found to yield constitutive expression of this operon, suggesting that iclR+ encodes a repressor protein. We have cloned iclR+ by taking advantage of its tight genetic linkage with the glyoxylate bypass operon. The clone complemented a mutant allele of iclR in trans, restoring an inducible phenotype for this operon. Deletion analysis identified a region of ca. 900 base pairs that was necessary and sufficient for complementation. The nucleotide sequence of the insert was then determined. Translation of this sequence revealed an open reading frame capable of encoding a protein with Mr 29,741 preceded by a potential Shine-Dalgarno ribosome-binding site. The deduced amino acid sequence includes a region at the amino terminus that may form a helix-turn-helix motif, a structure found in many DNA-binding domains.
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Affiliation(s)
- A Sunnarborg
- Department of Biochemistry, University of Minnesota, Minneapolis 55455
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15
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lac repressor: crystallization of intact tetramer and its complexes with inducer and operator DNA. Proc Natl Acad Sci U S A 1990; 87:1870-3. [PMID: 2408042 PMCID: PMC53585 DOI: 10.1073/pnas.87.5.1870] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The intact lac repressor tetramer, which regulates expression of the lac operon in Escherichia coli, has been crystallized in the native form, with an inducer, and in a ternary complex with operator DNA and an anti-inducer. The crystals without DNA diffract to better than 3.5 A. They belong to the monoclinic space group C2 and have cell dimensions a = 164.7 A, b = 75.6 A, and c = 161.2 A, with alpha = gamma = 90 degrees and beta = 125.5 degrees. Cocrystals have been obtained with a number of different lac operator-related DNA fragments. The complex with a blunt-ended 16-base-pair strand yielded tetragonal bipyramids that diffract to 6.5 A. These protein-DNA cocrystals crack upon exposure to the gratuitous inducer isopropyl beta-D-thiogalactoside, suggesting a conformational change in the repressor-operator complex.
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17
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Clore GM, Gronenborn AM. Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol 1989; 24:479-564. [PMID: 2676353 DOI: 10.3109/10409238909086962] [Citation(s) in RCA: 287] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has evolved over the last decade into a powerful method for determining three-dimensional structures of biological macromolecules in solution. Key advances have been the introduction of two-dimensional experiments, high-field superconducting magnets, and computational procedures for converting the NMR-derived interproton distances and torsion angles into three-dimensional structures. This article outlines the methodology employed, describes the major NMR experiments necessary for the spectral analysis of macromolecules, and discusses the computational approaches employed to date. The present state of the art is illustrated using a variety of examples, and future developments are indicated.
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Affiliation(s)
- G M Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
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18
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de Vlieg J, Berendsen HJ, van Gunsteren WF. An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution. Proteins 1989; 6:104-27. [PMID: 2622902 DOI: 10.1002/prot.340060203] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complex satisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator is based on many direct- and water-mediated hydrogen bonds and nonpolar contacts which allow the formation of a tight complex. No stable hydrogen bonds between side chains and bases are found, while specific contacts occur between both nonpolar groups and, to a lesser extent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, and chemically induced dynamic nuclear polarization (CIDNP) data.
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Affiliation(s)
- J de Vlieg
- Laboratory of Physical Chemistry, University of Groningen, Groningen, The Netherlands
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19
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Van de Ven FJ, Hilbers CW. Nucleic acids and nuclear magnetic resonance. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:1-38. [PMID: 3060357 DOI: 10.1111/j.1432-1033.1988.tb14425.x] [Citation(s) in RCA: 209] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- F J Van de Ven
- Department of Biophysical Chemistry, University of Nijmegen, The Netherlands
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20
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Hoffmann E, Rüterjans H. Two-dimensional 1H-NMR investigation of ribonuclease T1. Resonance assignments, secondary and low-resolution tertiary structures of ribonuclease T1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 177:539-60. [PMID: 3143569 DOI: 10.1111/j.1432-1033.1988.tb14406.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ribonuclease T1 was studied by two-dimensional 1H-NMR spectroscopy. Resonance assignments were obtained for the backbone protons of 95 amino acid residues and most of its side-chain protons using sequence-specific assignment procedures. The secondary structure elements of ribonuclease T1 were identified by an investigation of medium- and long-range nuclear Overhauser effects between the backbone and C beta protons. A low-resolution three-dimensional structure of ribonuclease T1 was deduced from qualitative interpretation of long-range nuclear Overhauser effects.
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Affiliation(s)
- E Hoffmann
- Institut für Biophysikalische Chemie, Johann-Wolfgang-Goethe-Universität, Frankfurt, Federal Republic of Germany
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21
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Brugge JA, Buchanan BG, Jardetzky O. Toward automating the process of determining polypeptide secondary structure from1H NMR data. J Comput Chem 1988. [DOI: 10.1002/jcc.540090612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Affiliation(s)
- R Kaptein
- Organic Chemistry Laboratory, University of Utrecht, The Netherlands
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23
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Kessler H, Gehrke M, Griesinger C. Zweidimensionale NMR-Spektroskopie, Grundlagen und Übersicht über die Experimente. Angew Chem Int Ed Engl 1988. [DOI: 10.1002/ange.19881000407] [Citation(s) in RCA: 169] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Kessler H, Gehrke M, Griesinger C. Two-Dimensional NMR Spectroscopy: Background and Overview of the Experiments [New Analytical Methods (36)]. ACTA ACUST UNITED AC 1988. [DOI: 10.1002/anie.198804901] [Citation(s) in RCA: 361] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Jelicks LA, Naider FR, Shenbagamurthi P, Becker JM, Broido MS. A type II beta-turn in a flexible peptide: proton assignment and conformational analysis of the alpha-factor from Saccharomyces cerevisiae in solution. Biopolymers 1988; 27:431-49. [PMID: 3282563 DOI: 10.1002/bip.360270307] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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26
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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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27
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Yada RY, Jackman RL, Nakai S. Secondary structure prediction and determination of proteins--a review. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1988; 31:98-108. [PMID: 3284835 DOI: 10.1111/j.1399-3011.1988.tb00011.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.
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Affiliation(s)
- R Y Yada
- Department of Food Science, University of Guelph, Ontario, Canada
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28
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Zuiderweg ER, Henkin J, Mollison KW, Carter GW, Greer J. Comparison of model and nuclear magnetic resonance structures for the human inflammatory protein C5a. Proteins 1988; 3:139-45. [PMID: 3255102 DOI: 10.1002/prot.340030302] [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: 01/04/2023]
Abstract
The model structure previously proposed for human C5a, based upon the crystal structure of the homologous protein human C3a, is compared to the solution structure of human C5a recently determined by nuclear magnetic resonance (NMR) methods in our laboratory. The general folding and helix topography of the C5a protein were modeled very well. The N-terminus, which is disordered in the C3a crystal, was correctly predicted in the C5a model both as to its being a helix and as to its docking site on the rest of the molecule. On the other hand, the NMR data show that the biologically important C-terminal residues are disordered in solution, unlike the model and the C3a crystal structure where this region was helical.
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Affiliation(s)
- E R Zuiderweg
- NMR Research Group, Abbott Laboratories, Abbott Park, Illinois 60064
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29
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de Vlieg J, Scheek RM, van Gunsteren WF, Berendsen HJ, Kaptein R, Thomason J. Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli. Proteins 1988; 3:209-18. [PMID: 3047742 DOI: 10.1002/prot.340030402] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 "hydrogen bond" distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints. Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.
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Affiliation(s)
- J de Vlieg
- Laboratory of Physical Chemistry, University of Groningen, The Netherlands
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30
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Weiss MA, Karplus M, Sauer RT. Quaternary structure and function in phage lambda repressor: 1H-NMR studies of genetically altered proteins. J Biomol Struct Dyn 1987; 5:539-56. [PMID: 2978735 DOI: 10.1080/07391102.1987.10506412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The quaternary structure and dynamics of phage lambda repressor are investigated in solution by 1H-NMR methods. lambda repressor contains two domains separable by proteolysis: an N-terminal domain that mediates sequence-specific DNA-A binding, and a C-terminal domain that contains strong dimer and higher-order contacts. The active species in operator recognition is a dimer. Although the crystal structure of an N-terminal fragment has been determined, the intact protein has not been crystallized, and there is little evidence concerning its structure. 1H-NMR data indicate that the N-terminal domain is only loosely tethered to the C-terminal domain, and that its tertiary structure is unperturbed by proteolysis of the "linker" polypeptide. It is further shown that in the intact repressor structure a quaternary interaction occurs between N-terminal domains. This domain-domain interaction is similar to the dimer contact observed in the crystal structure of the N-terminal fragment and involves the hydrophobic packing of symmetry-related helices (helix 5). In the intact structure this interaction is disrupted by the single amino-acid substitution, Ile84----Ser, which reduces operator affinity at least 100-fold. We conclude that quaternary interactions between N-terminal domains function to appropriately orient the DNA-binding surface with respect to successive major grooves of B-DNA.
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Affiliation(s)
- M A Weiss
- Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139
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31
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Braun W. Distance geometry and related methods for protein structure determination from NMR data. Q Rev Biophys 1987; 19:115-57. [PMID: 3310077 DOI: 10.1017/s0033583500004108] [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: 01/05/2023]
Abstract
Computational tools have been developed in the last few years, to allow a direct determination of protein structures from NMR data. Numerical calculations with simulated and experimental NMR constraints for distances and torsional angles show that data sets available with present NMR techniques carry enough information to determine reliably the global fold of a small protein. The maximum size of a protein for which the direct method can be applied is not limited by the computational tools but rather by the resolution of the two-dimensional spectra. A general estimate of the maximum size would be a molecular weight of about 10,000 (Markley et al. 1984), but parts of larger proteins might be accessible with the method. Effort for improvement of the NMR structures should be concentrated more on the local conformation rather than the global features. The r.m.s. D values for variations of the polypeptide backbone fold are on the order of 1.5-2 A for several of the studied proteins, indicating that the global structure is well determined by the present NMR data and their interpretation. The local structures are sometimes rather poor, with standard deviations for the backbone torsion angles of about 50 degrees. Possible improvements would be stereospecific resonance assignments of individual methylene protons and individual assignments of the methyl groups of the branched side-chains. Accurate estimates of the short-range NOE distance constraints by calibrating the distance constraints, including segmental flexibility effects, and combined use of distance geometry, energy minimization and molecular dynamics calculations, are further tools for improving the structures.
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Affiliation(s)
- W Braun
- Institut für Molekularbiologie u. Biophysik, Eidgenössische Technische Hochschule, Zürich, Switzerland
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32
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Culard F, Charlier M, Maurizot JC, Tardieu A. Lac repressor-Lac operator complexes. Solution X-ray scattering and electrophoretic studies. EUROPEAN BIOPHYSICS JOURNAL : EBJ 1987; 14:169-78. [PMID: 3549272 DOI: 10.1007/bf00253842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Complexes between the Lac repressor and a small DNA operator fragment (29 base pairs) were investigated using polyacrylamide gel electrophoresis and solution X-ray scattering. Titration of the DNA fragment with the repressor, followed by gel electrophoresis showed that only two types of complexes are formed with repressor/operator ratios of 0.5 and 2. Radii of gyration and forward scattered intensities were obtained from Guinier plots for repressor/operator ratios ranging from 0.3 to 2. They demonstrated that the first complex contains one repressor and two operators, whereas the second one contains four repressors and two operators. Mixing operator and repressor in equimolar concentrations leads to a mixture of both complexes. A possible model for the four repressor/two operator complex is proposed.
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33
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Kraulis PJ, Jones TA. Determination of three-dimensional protein structures from nuclear magnetic resonance data using fragments of known structures. Proteins 1987; 2:188-201. [PMID: 3447178 DOI: 10.1002/prot.340020304] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A method to build a three-dimensional protein model from nuclear magnetic resonance (NMR) data using fragments from a data base of crystallographically determined protein structures is presented. The interproton distances derived from the nuclear Overhauser effect (NOE) data are compared to the precalculated distances in the known protein structures. An efficient search algorithm is used, which arranges the distances in matrices akin to a C alpha diagonal distance plot, and compares the NOE distance matrices for short sequential zones of the protein to the data base matrices. After cluster analysis of the fragments found in this way, the structure is built by aligning fragments in overlapping zones. The sequentially long-range NOEs cannot be used in the initial fragments search but are vital to discriminate between several possible combinations of different groups of fragments. The method has been tested on one simulated NOE data set derived from a crystal structure and one experimental NMR data set. The method produces models that have good local structure, but may contain larger global errors. These models can be used as the starting point for further refinement, e.g., by restrained molecular dynamics or interactive graphics.
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Affiliation(s)
- P J Kraulis
- Department of Molecular Biology, Uppsala University, Sweden
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34
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Solving Solution Structural Problems by Combining 2-D NMR Data with Known Substructures from a Protein Database. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/978-3-642-71705-5_25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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35
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Montelione GT, Wüthrich K, Nice EC, Burgess AW, Scheraga HA. Identification of two anti-parallel beta-sheet conformations in the solution structure of murine epidermal growth factor by proton magnetic resonance. Proc Natl Acad Sci U S A 1986; 83:8594-8. [PMID: 3490668 PMCID: PMC386977 DOI: 10.1073/pnas.83.22.8594] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epidermal growth factor (EGF) is a small mitogenic protein. Proteins with sequence homology with EGF or with its membrane-bound protein receptor have been proposed to play a role in oncogenesis. This report describes solution NMR data that provide evidence that the solution conformation of murine EGF includes an anti-parallel beta-sheet structure involving residues S2-P4, V19-I23, and S28-N32; a small anti-parallel beta-sheet involving residues Y37-S38 and T44-R45; and a multiple-bend (or short irregular helix) structure for residues C6-C14 that is disulfide bonded to the V19-I23/S28-N32 beta-sheet. Implications of these results for structure and function studies of EGF and for molecular design of EGF and homologous alpha-type transforming growth factors are discussed.
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36
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37
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Weiss MA, Redfield AG, Griffey RH. Isotope-detected 1H NMR studies of proteins: a general strategy for editing interproton nuclear Overhauser effects by heteronuclear decoupling, with application to phage lambda repressor. Proc Natl Acad Sci U S A 1986; 83:1325-9. [PMID: 3006046 PMCID: PMC323068 DOI: 10.1073/pnas.83.5.1325] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A strategy for editing interproton nuclear Overhauser effects (NOEs) in proteins is proposed and illustrated. Selective incorporation of 13C- (or 15N)-labeled amino acids into a protein permits NOEs involving the labeled residues to be identified by heteronuclear difference decoupling. Such heteronuclear editing simplifies the NOE difference spectrum and avoids ambiguities due to spin diffusion. Isotope-detected 1H NMR thus opens to study proteins too large for conventional one- and two-dimensional NMR methods (20-75 kDa). We have applied this strategy to the N-terminal domain of phage lambda repressor, a protein of dimer molecular mass 23 kDa. A tertiary NOE from an internal aromatic ring (Phe-51) to a beta-13C-labeled alanine residue (Ala-62) is demonstrated.
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38
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Ebright RH. Evidence for a contact between glutamine-18 of lac repressor and base pair 7 of lac operator. Proc Natl Acad Sci U S A 1986; 83:303-7. [PMID: 3510433 PMCID: PMC322846 DOI: 10.1073/pnas.83.2.303] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Glutamine-18 of the lac repressor (lacR) has been substituted by glycine, by serine, and by leucine. The specificities of wild-type lacR and of the three substituted lacR variants have been analyzed with respect to base pairs 5, 6, 7, 8, 9, and 10 of the lac operator (lacO). The data indicate that [Gly18]lacR, [Ser18]lacR, and [Leu18]lacR lose the ability to distinguish between the O+ base pair G . C and the Oc base pairs T . A and A . T at position 7 of lacO (KdOc/KdO+ approximately equal to 1). In contrast, the three substituted variants retain the ability to discriminate O+ from Oc at each other position, by factors of 9 to 37. Therefore, I propose that glutamine-18 contacts base pair 7 of lacO. These data suggest that the interaction between the helix-turn-helix motif and DNA may be very similar or identical in lacR and the catabolite gene activator protein.
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39
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Kumar MR, Hosur RV, Roy KB, Miles HT, Govil G. Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC: altered conformations at BamHI cleavage sites. Biochemistry 1985; 24:7703-11. [PMID: 3004561 DOI: 10.1021/bi00347a030] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d-GGATCCGGATCC have been obtained by two-dimensional NMR methods and strategies derived from interproton distance calculations on different secondary structures of nucleic acids. Conformational details about the glycosidic dihedral angle and sugar pucker have been derived from the relative intensities of cross peaks in the two-dimensional J-correlated and nuclear Overhauser enhancement correlated spectra in D2O solution. It is observed that d-GGATCCGGATCC assumes a predominantly B-type conformation with sequence-dependent changes along the chain. The recognition site of BamHI shows a distinctly different geometrical environment. The sugar rings of G1 and G7 assume a C3'-endo geometry while the rest of the sugars possess C2'-endo geometry.
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40
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Zuiderweg ER, Scheek RM, Kaptein R. Two-dimensional 1H-nmr studies on the lac repressor DNA binding domain: further resonance assignments and identification of nuclear Overhauser enhancements. Biopolymers 1985; 24:2257-77. [PMID: 3912012 DOI: 10.1002/bip.360241208] [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: 01/08/2023]
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41
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Hahn U, Rüterjans H. Two-dimensional 1H NMR investigation of ribonuclease A and ribonuclease-A--pyrimidine-nucleotide complexes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 152:481-91. [PMID: 2996893 DOI: 10.1111/j.1432-1033.1985.tb09222.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ribonuclease A was studied by two-dimensional 1H NMR spectroscopy. 10 out of 12 alanine and 9 out of 10 threonine spin systems as well as all valine [9], leucine [2] and isoleucine [3] spin systems were identified from the correlated spectroscopy (COSY) and relayed coherence transfer spectroscopy (RCT). Sequence-specific assignments were obtained from nuclear Overhauser effect spectra for proton resonances of 21 amino acid moieties. 2' and 3'-pyrimidine-nucleotide-RNase-A complexes were also investigated by two-dimensional NMR. We were able to monitor structural changes in the active center, the vicinity of the active center and in regions far from the catalytic region. Chemical shift changes of resonances of protons near Thr-45 reflected the binding of the same moiety. This in turn is also dependent on the position of the nucleotide phosphate group. Binding of 2' nucleotides led to characteristic changes in protein regions not affected by the binding of 3' nucleotides. These results are interpreted in terms of structural differences between the 2' and 3'-nucleotide-RNase-A complexes; the structure of the complex of the native 3' nucleotide inhibitor being more closely related to that of the free protein.
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42
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Lane AN, Jardetzky O. NMR studies of the trp repressor from Escherichia coli. Characterisation and assignments of residue types. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 152:395-404. [PMID: 2996889 DOI: 10.1111/j.1432-1033.1985.tb09210.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
High-resolution proton nuclear magnetic resonance spectra of the trp repressor of Escherichia coli under various conditions are reported and analysed. The spectrum of the denatured state agrees with that predicted from the amino acid composition, with the exception of the two histidine residues, which have different chemical shifts although they titrate normally. The spectrum of the native protein shows the presence of extensive secondary and tertiary structure. Using information from chemical shifts, numbers of protons, titration behaviour, homonuclear chemical-shift-correlated spectroscopy and nuclear Overhauser enhancement correlated spectroscopy, most of the aromatic protons have been assigned to residue type. Further, about 30% of the aliphatic protons have been assigned to residue type by two-dimensional spectroscopy. Nuclear Overhauser enhancements establish that high-field methyl groups belonging to a valine residue lie directly over an aromatic ring.
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43
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Boelens R, Gros P, Scheek RM, Verpoorte JA, Kaptein R. Hydrogen exchange of individual amide protons in the E. coli lac repressor DNA-binding domain: a nuclear magnetic resonance study. J Biomol Struct Dyn 1985; 3:269-80. [PMID: 2855972 DOI: 10.1080/07391102.1985.10508416] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proton exchange in lac repressor headpiece was studied by COSY and 2D NOE spectroscopy. The exchange rates of amide protons, stabilized by the hydrogen bonds of the three alpha-helices of the headpiece, could be determined quantitatively. The exchange rates in these helices showed repetitive patterns of about three to four residues. A correlation with the position of the amide proton in the interior or the exterior of the alpha-helix of the protein was found. The exchange data strongly support the validity of the three-dimensional structure, as determined recently (Kaptein, R. et al., J. Mol. Biol. 182, 179-182 (1985)).
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Affiliation(s)
- R Boelens
- Department of Physical Chemistry, University of Groningen, The Netherlands
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44
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Ebright RH. Use of "loss-of-contact" substitutions to identify residues involved in an amino acid-base pair contact: effect of substitution of Gln18 of lac repressor by Gly, Ser, and Leu. J Biomol Struct Dyn 1985; 3:281-97. [PMID: 3917212 DOI: 10.1080/07391102.1985.10508417] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A procedure to identify which base pair of lac operator (lacO) a suspected contacting amino acid of Lac repressor (LacR) interacts with is presented. The procedure is to eliminate the ability of the amino acid under study to contact DNA, and then to determine at which base pair--if any--specificity is eliminated. To implement this procedure, four sets of Escherichia coli K-12 strains have been constructed. These strains permit: (i) the substitution of a selected amino acid of LacR by, respectively, Gly, Ser, Leu, or Gln, and (ii) the analysis of the specificity of the resulting substituted LacR with respect to base pairs 5, 6, 7, 8, 9, and 10 of lacO. This procedure has been applied to Gln18 of LacR. The preliminary data indicate that LacR (Gln18----Gly) is unable to distinguish between the O+ base pair G:C and the Oc base pair T:A at position 7 of lacO (KDOc/KDO+ = 0.93). In contrast, LacR(Gln18----Gly) discriminates O+ from Oc by a factor of 13 to 23 at each other position. The same qualitative pattern of results was obtained with LacR(Gln18----Ser) and LacR (Gln18----Leu). Therefore, I propose that Gln18 contacts base pair 7 of lacO. This proposal is consistent with the contact predicted in Ebright, R. in Protein Structure, Folding, and Design. D. Oxender ed., Alan R. Liss, New York (1985), in press.
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Affiliation(s)
- R H Ebright
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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45
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Neuhaus D, Wagner G, Vasák M, Kägi JH, Wüthrich K. Systematic application of high-resolution, phase-sensitive two-dimensional 1H-NMR techniques for the identification of the amino-acid-proton spin systems in proteins. Rabbit metallothionein-2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 151:257-73. [PMID: 2992961 DOI: 10.1111/j.1432-1033.1985.tb09096.x] [Citation(s) in RCA: 246] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Novel strategies for elucidation and classification of amino acid 1H-NMR spin systems in proteins were developed exploiting recently introduced two-dimensional NMR techniques such as phase-sensitive double-quantum-filtered correlated spectroscopy, relayed coherence transfer spectroscopy, double quantum spectroscopy and nuclear Overhauser spectroscopy. Due to the improved resolution in phase-sensitive spectra, the fine structure of cross peaks could be exploited as a powerful source of information for establishing 1H-1H connectivities. Principles for the interpretation of multiplet structures of absorption mode cross peaks are discussed. With these methods the 1H spin systems of rabbit liver metallothionein-2 were elucidated and classified according to amino acid types. Despite the intrinsically difficult situation arising from the unusual amino acid composition of this protein, a more complete characterization of the 1H spin systems prior to the step of sequential resonance assignments was achieved with the presently introduced methodology than was possible in earlier studies of proteins of similar size.
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46
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Interactive program for investigation of protein structures based on 1H NMR experiments. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0263-7855(85)80014-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Broido MS, James TL, Zon G, Keepers JW. Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two-dimensional nuclear Overhauser enhancement spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 150:117-28. [PMID: 2990923 DOI: 10.1111/j.1432-1033.1985.tb08996.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proton two-dimensional nuclear Overhauser enhancement (2D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)]2 in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 X 70 relaxation matrix including all proton dipole-dipole interactions and spin diffusion [Keepers, J. W. & James, T. L. (1984) J. Magn. Reson. 57, 404-426]. The theoretical spectra at each mixing time were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on the similarity of the six internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)]2, for which the crystal structure has been determined. Neither the standard B-form nor the energy-minimized structure will yield theoretical 2D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. However, many features of the experimental spectra can be represented by both the B-form and the energy-minimized structure. Sequence-dependent structural characteristics are manifest in the 2D NOE spectra, in particular at the purine-pyrimidine junction as noted previously in the crystal structure. On the whole, the energy-minimized structure appears to yield theoretical 2D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2D NOE data were consistent with nanosecond correction times as implied by proton spin-lattice relaxation time measurements. But better fits of some of the 2D NOE data using small variations in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.
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48
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Zuiderweg ERP, Boelens R, Kaptein R. Stereospecific assignments of1H-nmr methyl lines and conformation of valyl residues in thelac repressor headpiece. Biopolymers 1985. [DOI: 10.1002/bip.360240402] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Weber IT, Steitz TA. A model for the non-specific binding of catabolite gene activator protein to DNA. Nucleic Acids Res 1984; 12:8475-87. [PMID: 6390343 PMCID: PMC320391 DOI: 10.1093/nar/12.22.8475] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The binding of E. coli catabolite gene activator protein (CAP) to non-specific sequences of DNA has been modelled as an electrostatic interaction between four basic side chains of the CAP dimer and the charged phosphates of DNA. Calculation of the electrostatic contribution to the binding free energy at various separations of the two molecules shows that complex formation is favored when CAP and DNA are separated by as much as 12 A. Thus, the long range electrostatic interactions may provide the initial energy for complex formation and also the correct relative orientation of CAP and DNA. The non-specific complex does not involve the penetration of amino acid side chains into the major grooves of DNA and permits 'sliding' of the protein along DNA, which would enhance the rate of association of CAP with the specific site as has been proposed previously for lac repressor. We propose that, as it 'slides', CAP is moving in and out of the major grooves in order to sample the DNA sequence. Recognition of the specific DNA site is achieved by a complementarity in structure and hydrogen bonding between amino acids and the edges of base pairs exposed in the major grooves of DNA.
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50
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Weiss MA, Eliason JL, States DJ. Dynamic filtering by two-dimensional 1H NMR with application to phage lambda repressor. Proc Natl Acad Sci U S A 1984; 81:6019-23. [PMID: 6237367 PMCID: PMC391850 DOI: 10.1073/pnas.81.19.6019] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Flexible regions of proteins play an important role in catalysis, ligand binding, and macromolecular interactions. Because of its enhanced sensitivity to motional narrowing, two-dimensional coupling constant J-correlated 1H NMR may be used to observe these regions selectively. Dynamic filtering is an intrinsic feature of this experiment because cross-peak amplitude decays rapidly as linewidths approach the coupling constant. We demonstrate here the flexibility of the NH2-terminal arm of phage lambda repressor, which is thought to wrap around the double helix in the repressor-operator complex. The assignment of arm resonances is made possible by the construction of mutant repressor genes containing successive NH2-terminal deletions.
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