351
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Breslow E, Mombouyran V, Deeb R, Zheng C, Rose JP, Wang BC, Haschemeyer RH. Structural basis of neurophysin hormone specificity: Geometry, polarity, and polarizability in aromatic ring interactions. Protein Sci 1999; 8:820-31. [PMID: 10211828 PMCID: PMC2144317 DOI: 10.1110/ps.8.4.820] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The structural origins of the specificity of the neurophysin hormone-binding site for an aromatic residue in peptide position 2 were explored by analyzing the binding of a series of peptides in the context of the crystal structure of liganded neurophysin. A new modeling method for describing the van der Waals surface of binding sites assisted in the analysis. Particular attention was paid to the unusually large (5 kcal/mol) difference in binding free energy between Phe and Leu in position 2, a value representing more than three times the maximum expected based on hydrophobicity alone, and additionally remarkable since modeling indicated that the Leu side chain was readily accommodated by the binding pocket. Although evidence was obtained of a weak thermodynamic linkage between the binding interactions of the residue 2 side chain and of the peptide alpha-amino group, two factors are considered central. (1) The bound Leu side chain can establish only one-third of the van der Waals contacts available to a Phe side chain. (2) The bound Phe side chain appears to be additionally stabilized relative to Leu by more favorable dipole and induced dipole interactions with nonaromatic polar and sulfur ligands in the binding pocket, as evidenced by examination of its interactions in the pocket, analysis of the detailed energetics of transfer of Phe and Leu side chains from water to other phases, and comparison with thermodynamic and structural data for the binding of residue 1 side chains in this system. While such polar interactions of aromatic rings have been previously observed, the present results suggest their potential for significant thermodynamic contributions to protein structure and ligand recognition.
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Affiliation(s)
- E Breslow
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA.
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352
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Jaenicke R. Stability and folding of domain proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1999; 71:155-241. [PMID: 10097615 DOI: 10.1016/s0079-6107(98)00032-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- R Jaenicke
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
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353
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Abstract
Telomeres impart stability on linear eukaryotic chromosomes by acting as caps, preventing chromosomes from fusing together or being degraded. The structure of a telomere end binding protein in a complex with DNA provides the first molecular view of chromosome capping.
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Affiliation(s)
- D E Gottschling
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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354
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Murthy HM, Clum S, Padmanabhan R. Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. J Biol Chem 1999; 274:5573-80. [PMID: 10026173 DOI: 10.1074/jbc.274.9.5573] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The mosquito-borne dengue viruses are widespread human pathogens causing dengue fever, dengue hemorrhagic fever, and dengue shock syndrome, placing 40% of the world's population at risk with no effective treatment. The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B as a cofactor. We report here the crystal structure of the NS3 serine protease domain at 2.1 A resolution. This structure of the protease combined with modeling of peptide substrates into the active site suggests identities of residues involved in substrate recognition as well as providing a structural basis for several mutational effects on enzyme activity. This structure will be useful for development of specific inhibitors as therapeutics against dengue and other flaviviral proteases.
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Affiliation(s)
- H M Murthy
- Fels Institute, Temple University, Philadelphia, Pennsylvania 19140, USA.
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355
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Pang YP, Miller JL, Kollman PA. Computational and Experimental Studies of (2,2)-Bis(indol-1-yl-methyl)acetate Suggest the Importance of the Hydrophobic Effect in Aromatic Stacking Interactions. J Am Chem Soc 1999. [DOI: 10.1021/ja9828410] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan-Ping Pang
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Jennifer L. Miller
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
| | - Peter A. Kollman
- Contribution from the Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143
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356
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Schildbach JF, Karzai AW, Raumann BE, Sauer RT. Origins of DNA-binding specificity: role of protein contacts with the DNA backbone. Proc Natl Acad Sci U S A 1999; 96:811-7. [PMID: 9927650 PMCID: PMC15307 DOI: 10.1073/pnas.96.3.811] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/1998] [Indexed: 11/18/2022] Open
Abstract
A central question in protein-DNA recognition is the origin of the specificity that permits binding to the correct site in the presence of excess, nonspecific DNA. In the P22 Arc repressor, the Phe-10 side chain is part of the hydrophobic core of the free protein but rotates out to pack against the sugar-phosphate backbone of the DNA in the repressor-operator complex. Characterization of a library of position 10 variants reveals that Phe is the only residue that results in fully active Arc. One class of mutants folds stably but binds operator with reduced affinity; another class is unstable. FV10, one member of the first class, binds operator DNA and nonoperator DNA almost equally well. The affinity differences between FV10 and wild type indicate that each Phe-10 side chain contributes 1.5-2.0 kcal to operator binding but less than 0.5 kcal/mol to nonoperator binding, demonstrating that contacts between Phe-10 and the operator DNA backbone contribute to binding specificity. This appears to be a direct contribution as the crystal structure of the FV10 dimer is similar to wild type and the Phe-10-DNA backbone interactions are the only contacts perturbed in the cocrystal structure of the FV10-operator complex.
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Affiliation(s)
- J F Schildbach
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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357
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Wang XJ, Chen ZF, Kang BS, Liang H, Liu HQ, Yu KB, Su CY, Chen ZN. Chemistry of 2-mercaptophenol (H2mp) . Part iii. One dimensional arrays of binuclear anions of Mo (VI) linked by bis (2-hydroxyphenyl) disulfide via hydrogen bondings. Polyhedron 1999. [DOI: 10.1016/s0277-5387(98)00322-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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358
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Pappu RV, Schneller WJ, Weaver DL. Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(199606)17:8<1033::aid-jcc12>3.0.co;2-f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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359
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Boriack-Sjodin PA, Zeitlin S, Chen HH, Crenshaw L, Gross S, Dantanarayana A, Delgado P, May JA, Dean T, Christianson DW. Structural analysis of inhibitor binding to human carbonic anhydrase II. Protein Sci 1998; 7:2483-9. [PMID: 9865942 PMCID: PMC2143894 DOI: 10.1002/pro.5560071201] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
X-ray crystal structures of carbonic anhydrase II (CAII) complexed with sulfonamide inhibitors illuminate the structural determinants of high affinity binding in the nanomolar regime. The primary binding interaction is the coordination of a primary sulfonamide group to the active site zinc ion. Secondary interactions fine-tune tight binding in regions of the active site cavity >5 A away from zinc, and this work highlights three such features: (1) advantageous conformational restraints of a bicyclic thienothiazene-6-sulfonamide-1,1-dioxide inhibitor skeleton in comparison with a monocyclic 2,5-thiophenedisulfonamide skeleton; (2) optimal substituents attached to a secondary sulfonamide group targeted to interact with hydrophobic patches defined by Phe131, Leu198, and Pro202; and (3) optimal stereochemistry and configuration at the C-4 position of bicyclic thienothiazene-6-sulfonamides; the C-4 substituent can interact with His64, the catalytic proton shuttle. Structure-activity relationships rationalize affinity trends observed during the development of brinzolamide (Azopt), the newest carbonic anhydrase inhibitor approved for the treatment of glaucoma.
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Affiliation(s)
- P A Boriack-Sjodin
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA
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360
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Lesburg CA, Caruthers JM, Paschall CM, Christianson DW. Managing and manipulating carbocations in biology: terpenoid cyclase structure and mechanism. Curr Opin Struct Biol 1998; 8:695-703. [PMID: 9914250 DOI: 10.1016/s0959-440x(98)80088-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Terpenoid cyclases catalyze remarkably complex cyclization cascades that are initiated by the formation of a highly reactive carbocation in a polyisoprene substrate. Recent crystal structures of terpenoid cyclases show how these enzymes provide a template for binding and stabilizing the flexible substrate in the precise orientation required for catalysis, trigger carbocation formation, chaperone the conformations of the reactive carbocation intermediates through a unique cyclization sequence, and sequester and stabilize carbocations from premature quenching. Notably, terpenoid cyclases and catalytic antibodies have converged to similar chemical and structural strategies for managing highly reactive carbocations in polyisoprene cyclization cascades.
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Affiliation(s)
- C A Lesburg
- Department of Structural Chemistry Schering-Plough Research Institute 2015 Galloping Hill Road Kenilworth NJ 07033-0539 USA
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361
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Hutchinson EG, Sessions RB, Thornton JM, Woolfson DN. Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci 1998; 7:2287-300. [PMID: 9827995 PMCID: PMC2143855 DOI: 10.1002/pro.5560071106] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Antiparallel beta-sheets present two distinct environments to inter-strand residue pairs: beta(A,HB) sites have two backbone hydrogen bonds; whereas at beta(A,NHB) positions backbone hydrogen bonding is precluded. We used statistical methods to compare the frequencies of amino acid pairs at each site. Only approximately 10% of the 210 possible pairs showed occupancies that differed significantly between the two sites. Trends were clear in the preferred pairs, and these could be explained using stereochemical arguments. Cys-Cys, Aromatic-Pro, Thr-Thr, and Val-Val pairs all preferred the beta(A,NHB) site. In each case, the residues usually adopted sterically favored chi1 conformations, which facilitated intra-pair interactions: Cys-Cys pairs formed disulfide bonds; Thr-Thr pairs made hydrogen bonds; Aromatic-Pro and Val-Val pairs formed close van der Waals contacts. In contrast, to make intimate interactions at a beta(A,HB) site, one or both residues had to adopt less favored chi1 geometries. Nonetheless, pairs containing glycine and/or aromatic residues were favored at this site. Where glycine and aromatic side chains combined, the aromatic residue usually adopted the gauche conformation, which promoted novel aromatic ring-peptide interactions. This work provides rules that link protein sequence and tertiary structure, which will be useful in protein modeling, redesign, and de novo design. Our findings are discussed in light of previous analyses and experimental studies.
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Affiliation(s)
- E G Hutchinson
- Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
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362
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Hansen VM, Ma AK, Biradha K, Pomeroy RK, Zaworotko MJ. Conformational Isomerism in Triosmium Clusters: Structures of Yellow and Red Os3(CO)11[P(p-C6H4F)3] and Os3(CO)11(PBut3). Organometallics 1998. [DOI: 10.1021/om980365g] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valerie. M. Hansen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6, and Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Andrew K. Ma
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6, and Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Kumar Biradha
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6, and Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Roland K. Pomeroy
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6, and Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Michael J. Zaworotko
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6, and Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
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363
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Kim EI, Paliwal S, Wilcox CS. Measurements of Molecular Electrostatic Field Effects in Edge-to-Face Aromatic Interactions and CH-π Interactions with Implications for Protein Folding and Molecular Recognition. J Am Chem Soc 1998. [DOI: 10.1021/ja982620u] [Citation(s) in RCA: 290] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eun-il Kim
- Department of Chemistry University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Sunil Paliwal
- Department of Chemistry University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Craig S. Wilcox
- Department of Chemistry University of Pittsburgh Pittsburgh, Pennsylvania 15260
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364
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Welsh LC, Symmons MF, Sturtevant JM, Marvin DA, Perham RN. Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution. J Mol Biol 1998; 283:155-77. [PMID: 9761681 DOI: 10.1006/jmbi.1998.2081] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of alpha-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely alpha-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.
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Affiliation(s)
- L C Welsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
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365
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Galemmo RA, Maduskuie TP, Dominguez C, Rossi KA, Knabb RM, Wexler RR, Stouten PF. The de novo design and synthesis of cyclic urea inhibitors of factor Xa: initial SAR studies. Bioorg Med Chem Lett 1998; 8:2705-10. [PMID: 9873607 DOI: 10.1016/s0960-894x(98)00471-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this report we discuss the design, synthesis, and validation of a novel series of cyclic urea inhibitors of the blood coagulation protein Factor Xa. This work culminates in compound 11, a monoamidine inhibitor of fXa employing a new S4 ligand that reduces the cationic character of these analogs. Compound 11 represents a lead for a series of more potent and selective inhibitors.
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Affiliation(s)
- R A Galemmo
- DuPont Pharmaceuticals Company, Wilmington, DE 19880-0500, USA
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366
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Jaśkiewicz A, Lis K, Rózycki J, Kupryszewski G, Rolka K, Ragnarsson U, Zbyryt T, Wilusz T. Modifications outside the proteinase binding loop in Cucurbita maxima trypsin inhibitor III (CMTI-III) analogues change the binding energy with bovine beta-trypsin. FEBS Lett 1998; 436:174-8. [PMID: 9781673 DOI: 10.1016/s0014-5793(98)01119-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Five 26-peptide analogues of the trypsin inhibitor [Pro18]CMTI-III containing Leu or Tyr in position 7 and Val or Tyr in position 27: 1 (Leu7, Tyr27), 2 (Tyr7, Val27), 3 (Tyr7, Tyr27), 4 (Leu7, Val27) and 5 (Leu7, Ala18, Tyr27) were synthesized by the solid-phase method. Analogues 1-4 displayed Ka with bovine beta-trypsin of the same order of magnitude as the wild CMTI-III inhibitor, whereas for analogue 5, this value was lower by about 3 orders of magnitude. This indicated that for the analogues with Pro (but not with Ala) in position 18, the side-chain interactions between positions 7 and 27 did not play a critical role for the stabilization of the active structure. In addition, these results also suggest that Tyr7 is involved in an additional aromatic interaction with position 41 of the enzyme.
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Affiliation(s)
- A Jaśkiewicz
- Faculty of Chemistry, University of Gdańsk, Poland
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367
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Abstract
The properties of the complexes of ferricytochrome c with two different polyanions--poly(vinylsulfate) and poly(4-styrene-sulfonate)--with a comparable charge density but with the different size of the uncharged part of their molecules have been studied by means of optical spectroscopy, differential scanning colorimetry, and gel chromatography. Ferriccytochrome c formed a complex with the former one through coulombic interactions and remained in a native-like state. The addition of the second polyanion to a solution of ferric cytochrome c at a low ionic strength, pH 7.0, resulted in profound conformational change in the hydrophobic core of protein (opening of the heme crevice with a perturbation of the methionine 80-heme iron bond and the hydrophobic core of the protein). These may be understood as an involvement of noncoulombic (hydrophobic, H-bonding) interactions of the uncharged part of the polyanion molecule. Conformational changes and the observed shift in acidic transition from low spin to high spin state of ferric cytochrome c detected in the presence of the polyanions may have biological implication in understanding the origin of conformational changes in proteins induced in the course of their interaction with membrane lipids and membrane proteins.
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Affiliation(s)
- E Sedlák
- Department of Biochemistry, Faculty of Science, P. J. Safárik University, Kosice, Slovakia
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368
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Laberge M. Intrinsic protein electric fields: basic non-covalent interactions and relationship to protein-induced Stark effects. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:305-30. [PMID: 9733989 DOI: 10.1016/s0167-4838(98)00100-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Knowledge of the interactions involving charged, polar and polarizable groups in proteins is fundamental, not only because they are important determinants for gaining insight into biophysical molecular recognition and assembly processes, but also for understanding how the matrix of a protein can be viewed as an electric field capable of inducing Stark perturbations on the spectral properties of biological optical centers. This review describes the essential features of noncovalent interactions in protein systems and discusses the concept of the dielectric constant of a protein in the context of different microscopic and macroscopic modeling approaches. It also provides an account of a specific type of high resolution vibrational and optical Stark spectroscopy attempting to correlate the observed spectral properties of biological optical centers to the intrinsic protein fields induced by the matrix in which they reside.
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Affiliation(s)
- M Laberge
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104, USA.
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369
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Sundholm D, Sundberg MR, Uggla R. Intermolecular Interactions in p-Chlorobenzoic Acid Dimers. J Phys Chem A 1998. [DOI: 10.1021/jp9813589] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dage Sundholm
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Markku R. Sundberg
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
| | - Rolf Uggla
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
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370
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Wheat β-amylase behaviour regarding salt promoted adsorption processes. Chromatographia 1998. [DOI: 10.1007/bf02467673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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371
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Conti E, Uy M, Leighton L, Blobel G, Kuriyan J. Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 1998; 94:193-204. [PMID: 9695948 DOI: 10.1016/s0092-8674(00)81419-1] [Citation(s) in RCA: 638] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Selective nuclear import is mediated by nuclear localization signals (NLSs) and cognate transport factors known as karyopherins or importins. Karyopherin alpha recognizes "classical" monopartite and bipartite NLSs. We report the crystal structure of a 50 kDa fragment of the 60 kDa yeast karyopherin alpha, in the absence and presence of a monopartite NLS peptide at 2.2 A and 2.8 A resolution, respectively. The structure shows a tandem array of ten armadillo repeats, organized in a right-handed superhelix of helices. Binding of the NLS peptide occurs at two sites within a helical surface groove that is lined by conserved residues. The structure reveals the determinants of NLS specificity and suggests a model for the recognition of bipartite NLSs.
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Affiliation(s)
- E Conti
- Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA
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372
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373
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Zoltewicz JA, Maier NM, Fabian WMF. π-Cation and π-Dipole-Stabilizing Interactions in a Simple Model System with Cofacial Aromatic Rings. J Org Chem 1998. [DOI: 10.1021/jo9801465] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John A. Zoltewicz
- Department of Chemistry, University of Florida, Gainesville, Forida 32611-7200
| | - Norbert M. Maier
- Department of Chemistry, University of Florida, Gainesville, Forida 32611-7200
| | - Walter M. F. Fabian
- Institut für Organische Chemie, Karl-Franzens Universität, A-8010 Graz, Austria
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374
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Gigoux V, Escrieut C, Silvente-Poirot S, Maigret B, Gouilleux L, Fehrentz JA, Gully D, Moroder L, Vaysse N, Fourmy D. Met-195 of the cholecystokinin-A receptor interacts with the sulfated tyrosine of cholecystokinin and is crucial for receptor transition to high affinity state. J Biol Chem 1998; 273:14380-6. [PMID: 9603948 DOI: 10.1074/jbc.273.23.14380] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sulfation of the tyrosine at the seventh position from the C terminus of cholecystokinin (CCK) is crucial for CCK binding to the CCK-A receptor. Using three-dimensional modeling, we identified methionine 195 of the CCK-A receptor as a putative amino acid in interaction with the aromatic ring of the sulfated tyrosine of CCK. We analyzed the role played by the two partners of this interaction. The exchange of Met-195 for a leucine caused a minor decrease (2. 8-fold) on the affinity of the high affinity sites for sulfated CCK-9, a strong drop (73%) of their number, and a 30-fold decrease on the affinity of the low and very low affinity sites for sulfated CCK-9, with no change in their number. The mutation also caused a 54-fold decrease of the potency of the receptor to induce inositol phosphates production. The high affinity sites of the wild-type CCK-A receptor were highly selective (800-fold) toward sulfated versus nonsulfated CCK, whereas low and very low affinity sites were poorly selective (10- and 18-fold). In addition, the M195L mutant bound, and responded to, sulfated CCK analogues with decreased affinities and potencies, whereas it bound and responded to nonsulfated CCK identically to the wild-type receptor. Thus, Met-195 interacts with the aromatic ring of the sulfated tyrosine to correctly position the sulfated group of CCK in the binding site of the receptor. This interaction is essential for CCK-dependent transition of the CCK-A receptor to a high affinity state. Our data should represent an important step toward the identification of the residue(s) of the receptor in interaction with the sulfate moiety of CCK and the understanding of the molecular mechanisms that govern CCK-A receptor activation.
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Affiliation(s)
- V Gigoux
- INSERM U151, Institut Louis Bugnard, CHU de Rangueil, Bat. L3, 31403 Toulouse Cedex, France
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375
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Pal D, Chakrabarti P. Different types of interactions involving cysteine sulfhydryl group in proteins. J Biomol Struct Dyn 1998; 15:1059-72. [PMID: 9669552 DOI: 10.1080/07391102.1998.10509001] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Various types of interactions involving the sulfhydryl group of free cysteine residues have been analyzed using known protein structures. In a hydrogen bond the -SH group is more amenable to donating its proton to a carbonyl group, rather than acting as a proton acceptor. It rarely interacts with a carboxylate group, and is a poor ligand to bind an anionic substrate. It is quite prone to make contacts that are definitely non-hydrogen bond type. In the S...C=O interaction the S atom is placed on the face of an amide group (mostly from the main-chain, but there are cases from the side-chain also) close to the C atom. Cases of S...N interaction, where the S atom is on top of the N atom of another residue (both main-, as well as side-chains, including the guanidinium group) are also observed. A considerable number of Cys residues have aromatic residues as neighbors, and here too, the preferred mode of interaction is along the face. The intra-residue S...C=O interaction constrains the main-chain and side-chain torsion angles (psi and chi1), whereas the inter-residue interactions are non-local and stabilize the tertiary structure. The S...C=O interaction may have a role in lowering the pKa values of the Cys residues in enzyme active sites.
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Affiliation(s)
- D Pal
- Department of Biochemistry, Bose Institute, CIT Scheme VIIM, Calcutta, India
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376
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377
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Wang B, Jones DN, Kaine BP, Weiss MA. High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure 1998; 6:555-69. [PMID: 9634694 DOI: 10.1016/s0969-2126(98)00058-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Transcriptional initiation and elongation provide control points in gene expression. Eukaryotic RNA polymerase II subunit 9 (RPB9) regulates start-site selection and elongational arrest. RPB9 contains Cys4 Zn(2+)-binding motifs which are conserved in archaea and homologous to those of the general transcription factors TFIIB and TFIIS. RESULTS The structure of an RPB9 domain from the hyperthermophilic archaeon Thermococcus celer was determined at high resolution by NMR spectroscopy. The structure consists of an apical tetrahedral Zn(2+)-binding site, central beta sheet and disordered loop. Although the structure lacks a globular hydrophobic core, the two surfaces of the beta sheet each contain well ordered aromatic rings engaged in serial edge-to-face interactions. Basic sidechains are clustered near the Zn(2+)-binding site. The disordered loop contains sidechains conserved in TFIIS, including acidic residues essential for the stimulation of transcriptional elongation. CONCLUSIONS The planar architecture of the RPB9 zinc ribbon-distinct from that of a conventional globular domain-can accommodate significant differences in the alignment of polar, non-polar and charged sidechains. Such divergence is associated with local and non-local changes in structure. The RPB9 structure is distinguished by a fourth beta strand (extending the central beta sheet) in a well ordered N-terminal segment and also differs from TFIIS (but not TFIIB) in the orientation of its apical Zn(2+)-binding site. Cys4 Zn(2+)-binding sites with distinct patterns of polar, non-polar and charged residues are conserved among unrelated RNAP subunits and predicted to form variant zinc ribbons.
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Affiliation(s)
- B Wang
- Department of Chemistry, Center for Molecular Oncology, University of Chicago, Illinois 60637-5419, USA
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378
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Umezawa Y, Tsuboyama S, Honda K, Uzawa J, Nishio M. CH/πInteraction in the Crystal Structure of Organic Compounds. A Database Study. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1998. [DOI: 10.1246/bcsj.71.1207] [Citation(s) in RCA: 330] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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379
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Abstract
It is now generally accepted that the presence of 5-methylcytosine (5mC) in human DNA has both a genetic and an epigenetic effect on cellular development, differentiation and transformation. First, 5mC is more unstable than its unmethylated counterpart cytosine. Hydrolytic deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-->T transition mutation. Sites of DNA methylation are mutational hotspots in many human tumors. Second, DNA methylation of promoter regions is often correlated with the down regulation of the corresponding gene. Both of these effects have fundamental consequences for basic functions of the cell like cellular differentiation, the development of cancer and possibly other diseases, and on the evolutionary process. Recent hypotheses also propose a role for methylation in the process of aging. In this review we will describe recent findings and hypotheses about the function of 5mC in DNA with the focus on its involvement in human carcinogenesis.
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Affiliation(s)
- C Schmutte
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA 19107, USA
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380
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Berna PP, Berna N, Porath J, Oscarsson S. Comparison of the protein adsorption selectivity of salt-promoted agarose-based adsorbents. Hydrophobic, thiophilic and electron donor-acceptor adsorbents. J Chromatogr A 1998; 800:151-9. [PMID: 9561759 DOI: 10.1016/s0021-9673(97)01130-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein adsorption of human serum onto six different agarose-based chromatographic gels that were representative of the salt-promoted adsorbent family [octyl- and phenyl-Sepharose, mercaptoethanol-divinyl sulfone agarose (T gel), mercaptomethylene pyridine-derivatized agarose gel (MP gel), tricyanoaminopropene-divinyl sulfone agarose (DVS-TCP gel), tricyanoamino-propene-bisoxirane agarose (bisoxirane-TCP gel)] was studied in the presence of moderate or high concentrations of the water structuring salt, sodium sulfate. Study of the protein adsorption selectivity by two-dimensional gel electrophoresis revealed an opposed selectivity for hydrophobic interaction adsorbents and electron donor-acceptor adsorbents. The T gel, MP gel and TCP gels belonged to the electron donor-acceptor adsorbents, displaying a main selectivity for immunoglobulins, whereas octyl-Sepharose belonged to the hydrophobic adsorbents, displaying a main selectivity for 'hydrophobic' proteins. Phenyl-Sepharose for its part was described as an example of a composite selectivity of both families. The conclusion of this work is two-fold: (1) hydrophobic interaction chromatography (HIC) and electron donor-acceptor chromatography (EDAC) have opposed protein selectivities and are both salt-promoted. As a main consequence, it means that high concentrations of a water-structuring salt can promote different types of weak molecular interactions, resulting in different protein adsorption selectivities: (2) thiophilic adsorption chromatography (TAC) should be renamed EDAC as similar protein selectivity is demonstrated for electron donor-acceptor ligand devoid of sulfur atoms.
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Affiliation(s)
- P P Berna
- Biochemical Separation Centre, University of Uppsala, BMC, Sweden
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381
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Ranganathan D, Haridas V, Karle IL. Cystinophanes, a Novel Family of Aromatic-Bridged Cystine Cyclic Peptides: Synthesis, Crystal Structure, Molecular Recognition, and Conformational Studies. J Am Chem Soc 1998. [DOI: 10.1021/ja9734915] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darshan Ranganathan
- Contribution from the Biomolecular Research Unit, Regional Research Laboratory (CSIR), Trivandrum 695019, India, and the Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - V. Haridas
- Contribution from the Biomolecular Research Unit, Regional Research Laboratory (CSIR), Trivandrum 695019, India, and the Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
| | - Isabella L. Karle
- Contribution from the Biomolecular Research Unit, Regional Research Laboratory (CSIR), Trivandrum 695019, India, and the Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, D.C. 20375-5341
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382
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Steiner T. The terminal alkynes. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1087-3295(98)80004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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383
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Puius YA, Zhao Y, Sullivan M, Lawrence DS, Almo SC, Zhang ZY. Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc Natl Acad Sci U S A 1997; 94:13420-5. [PMID: 9391040 PMCID: PMC28320 DOI: 10.1073/pnas.94.25.13420] [Citation(s) in RCA: 344] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.
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Affiliation(s)
- Y A Puius
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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384
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Zographos SE, Oikonomakos NG, Tsitsanou KE, Leonidas DD, Chrysina ED, Skamnaki VT, Bischoff H, Goldmann S, Watson KA, Johnson LN. The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor. Structure 1997; 5:1413-25. [PMID: 9384557 DOI: 10.1016/s0969-2126(97)00292-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND In muscle and liver, glycogen concentrations are regulated by the reciprocal activities of glycogen phosphorylase (GP) and glycogen synthase. An alkyl-dihydropyridine-dicarboxylic acid has been found to be a potent inhibitor of GP, and as such has potential to contribute to the regulation of glycogen metabolism in the non-insulin-dependent diabetes diseased state. The inhibitor has no structural similarity to the natural regulators of GP. We have carried out structural studies in order to elucidate the mechanism of inhibition. RESULTS Kinetic studies with rabbit muscle glycogen phosphorylase b (GPb) show that the compound (-)(S)-3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5, 6-tricarboxylate (Bay W1807) has a Ki = 1.6 nM and is a competitive inhibitor with respect to AMP. The structure of the cocrystallised GPb-W1807 complex has been determined at 100K to 2.3 A resolution and refined to an R factor of 0.198 (Rfree = 0.287). W1807 binds at the GPb allosteric effector site, the site which binds AMP, glucose-6-phosphate and a number of other phosphorylated ligands, and induces conformational changes that are characteristic of those observed with the naturally occurring allosteric inhibitor, glucose-6-phosphate. The dihydropyridine-5,6-dicarboxylate groups mimic the phosphate group of ligands that bind to the allosteric site and contact three arginine residues. CONCLUSIONS The high affinity of W1807 for GP appears to arise from the numerous nonpolar interactions made between the ligand and the protein. Its potency as an inhibitor results from the induced conformational changes that lock the enzyme in a conformation known as the T' state. Allosteric enzymes, such as GP, offer a new strategy for structure-based drug design in which the allosteric site can be exploited. The results reported here may have important implications in the design of new therapeutic compounds.
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Affiliation(s)
- S E Zographos
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation 48, vas Constantinou Avenue, Athens, 11635, Greece
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385
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Feller G, Arpigny J, Narinx E, Gerday C. Molecular adaptations of enzymes from psychrophilic organisms. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0300-9629(97)00011-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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386
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Potrzebowski MJ, Blaszczyk J, Wieczorek MW, Klinowski J. Solid-State NMR and X-ray Diffraction Studies of the Geometry and Intramolecular Dynamics of Bis(organothiophosphoryl) Dichalcogenides. J Phys Chem A 1997. [DOI: 10.1021/jp9639760] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-362 Lódz, Poland, Institute of Technical Biochemistry, Technical University of Lódz, Stefanowskiego 4/10, 90−924 Lódz, Poland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jaroslaw Blaszczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-362 Lódz, Poland, Institute of Technical Biochemistry, Technical University of Lódz, Stefanowskiego 4/10, 90−924 Lódz, Poland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michal W. Wieczorek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-362 Lódz, Poland, Institute of Technical Biochemistry, Technical University of Lódz, Stefanowskiego 4/10, 90−924 Lódz, Poland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jacek Klinowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-362 Lódz, Poland, Institute of Technical Biochemistry, Technical University of Lódz, Stefanowskiego 4/10, 90−924 Lódz, Poland, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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387
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Brisbois RG, Fogel LE, Nicaise OJC, DeWeerd PJ. Regiocontrolled Synthesis of CpCo-Cyclobutadienyl-Bridged p-Cyclophanes via Annulation of Acyclic Diynes. J Org Chem 1997. [DOI: 10.1021/jo971022f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ronald G. Brisbois
- Department of Chemistry, Hamline University, 1536 Hewitt Avenue, St. Paul, Minnesota 55104-1284
| | - Louis E. Fogel
- Department of Chemistry, Hamline University, 1536 Hewitt Avenue, St. Paul, Minnesota 55104-1284
| | - Olivier J.- C. Nicaise
- Department of Chemistry, Hamline University, 1536 Hewitt Avenue, St. Paul, Minnesota 55104-1284
| | - Peter J. DeWeerd
- Department of Chemistry, Hamline University, 1536 Hewitt Avenue, St. Paul, Minnesota 55104-1284
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388
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Lesburg CA, Zhai G, Cane DE, Christianson DW. Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology. Science 1997; 277:1820-4. [PMID: 9295272 DOI: 10.1126/science.277.5333.1820] [Citation(s) in RCA: 325] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The crystal structure of pentalenene synthase at 2.6 angstrom resolution reveals critical active site features responsible for the cyclization of farnesyl diphosphate into the tricyclic hydrocarbon pentalenene. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. The core active site structure of the enzyme may be preserved among the greater family of terpenoid synthases, possibly implying divergence from a common ancestral synthase to satisfy biological requirements for increasingly diverse natural products.
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Affiliation(s)
- C A Lesburg
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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389
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Mérienne K, Germain N, Zinn-Justin S, Boulain JC, Ducancel F, Ménez A. The functional architecture of an acetylcholine receptor-mimicking antibody. J Biol Chem 1997; 272:23775-83. [PMID: 9295323 DOI: 10.1074/jbc.272.38.23775] [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: 02/05/2023] Open
Abstract
Malpha2-3 is a monoclonal antibody that partially mimics the nicotinic acetylcholine receptor (AChR). Its three-dimensional structure has been previously predicted by molecular modeling, suggesting that 29 complementarity determining region (CDR) residues and 2 framework residues are exposed to solvent. To identify the antibody residues that bind to the antigen, i.e. snake toxin that binds specifically to AChR, we (i) produced the scFv form of Malpha2-3 fused to alkaline phosphatase, in the periplasmic space of Escherichia coli; (ii) submitted approximately 75% of exposed residues of the fused scFv to individual or combined mutations, and (iii) identified the residues whose mutations affect scFv binding to the toxin, using a sensitive enzyme-linked immunosorbent assay. 11 critical residues were identified, including 8 heavy chain residues, 2 framework residues, and 1 light chain residue. They cover a surface of approximately 800 A2, with a subset of most critical residues (VHD31, VHY32, and VHG101) and several aromatic residues. This functional architecture not only constitutes a plausible complementary binding surface for the snake toxin but also offers a structural basis to ultimately understand the capacity of the antibody to partially mimic AChR.
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Affiliation(s)
- K Mérienne
- Département d'Ingénierie et d'Etudes des Protéines, Direction des Sciences du Vivant, Commissariat à l'Energie Atomique, Saclay, 91191 Gif-sur-Yvette Cedex, France
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390
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Yang YK, Dickinson C, Haskell-Luevano C, Gantz I. Molecular basis for the interaction of [Nle4,D-Phe7]melanocyte stimulating hormone with the human melanocortin-1 receptor. J Biol Chem 1997; 272:23000-10. [PMID: 9287296 DOI: 10.1074/jbc.272.37.23000] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The melanocortin-1 receptor (MC1R) is a seven-transmembrane (TM) G-protein-coupled receptor whose natural ligands are the melanocortin peptides, adrenocorticotropic hormone, and alpha-, beta-, and gamma- melanocyte stimulating hormone (MSH). To test a previously constructed three-dimensional model of the molecular interaction between the long-acting, superpotent alpha-MSH analog [Nle4,D-Phe7]MSH (NDP-MSH) and the human MC1R we examined the effects of site-directed receptor mutagenesis on the binding affinity and potency of NDP-MSH. In addition, we also examined the effects of these same mutations on the binding affinity and potency of the structurally related agonists alpha-MSH, gamma-MSH, and Ac-Nle4-cyclic-[Asp5,His6,D-Phe7,Arg8,Trp9,Lys10]NH2 (MT-II). Mutagenesis of acidic receptor residues Glu94 in TM2 and Asp117 or Asp121 in TM3 significantly altered the binding affinity and potency of all four agonists suggesting that these receptor residues are important to the ligand-receptor interactions of all. A disproportionate change in agonist potency versus affinity observed with simultaneous mutation of these acidic residues (mutant constructs D117A/D121A or E94A/D117A/D121A) or introduction of a single positive charge (mutant construct D121K) also implicates these residues in receptor activation. In addition, results from the individual mutation of aromatic receptor residues Phe175, Phe196, and Phe257, and simultaneous mutation of multiple TM4, -5, and -6 tyrosine and phenylalanine residues suggests that aromatic-aromatic ligand-receptor interactions also participate in binding these melanocortins to the MC1R. These experiments appear to have identified some of the critical receptor residues involved in the ligand-receptor interactions between these melanocortins and the hMC1R.
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Affiliation(s)
- Y k Yang
- Department of Internal Medicine, University of Michigan Medical School and Veterans Administration Medical Center, Ann Arbor, Michigan 48109-0682, USA
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391
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Gromiha MM, Selvaraj S. Influence of medium and long range interactions in different structural classes of globular proteins. J Biol Phys 1997; 23:151-62. [PMID: 23345657 PMCID: PMC3456391 DOI: 10.1023/a:1004981409616] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An analysis of the dependence known three dimensional structure ofglobular proteins on their residue contacts and their interactions providesmuch information about their folding and stability. In this work, we analysethe residue-residue contacts and the role of medium and long rangeinteractions in globular proteins belonging to different structural classes.The results show that while medium range interactions predominate in allalpha class proteins, long range interactions predominate in all beta class.The residues Pro and Gly are found to have lowest medium range contacts,probably due to their helix breaking tendency. The hydrophobic residues Ile,Val and Tyr have higher long range contacts, and hence may serve as goodnucleation centres. Further, the role of charged residues and disulfidebridges in these interactions are also discussed.
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Affiliation(s)
- M M Gromiha
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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392
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Kopka ML, Goodsell DS, Han GW, Chiu TK, Lown JW, Dickerson RE. Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G. Structure 1997; 5:1033-46. [PMID: 9309219 DOI: 10.1016/s0969-2126(97)00255-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Polyamide drugs, such as netropsin, distamycin and their lexitropsin derivatives, can be inserted into a narrow B-DNA minor groove to form 1:1 complexes that can distinguish AT base pairs from GC, but cannot detect end-for-end base-pair reversals such as TA for AT. In contrast, 2:1 side-by-side polyamide drug complexes potentially are capable of such discrimination. Imidazole (Im) and pyrrole (Py) rings side-by-side read a GC base pair with the Im ring recognizing the guanine side. But the reason for this specific G-Im association is unclear because the guanine NH2 group sits in the center of the groove. A 2:1 drug:DNA complex that presents Im at both ends of a GC base pair should help unscramble the issue of imidazole reading specificity. RESULTS We have determined the crystal structure of a 2:1 complex of a di-imidazole lexitropsin (DIM), an analogue of distamycin, and a DNA decamer with the sequence C-A-T-G-G-C-C-A-T-G. The two DIM molecules sit antiparallel to one another in a broad minor groove, with their cationic tails widely separated. Im rings of one drug molecule stack against amide groups of the other. DIM1 rests against nucleotides C7A8T9G10 of strand 1 of the helix, whereas DIM2 rests against G14G15C16C17 on strand 2. All DIM amide nitrogens donate hydrogen bonds to N and O atoms on the floor of the DNA groove and, in addition, the two Im rings on DIM2 accept hydrogen bonds from guanine N2 amines, thereby providing specific reading. The guanine N2 amine can bond to Im on its own side of the groove, but not on the cytosine side, because of limits on close approach of the two Im rings and the geometry of sp2 hybridization about the amide nitrogen. CONCLUSIONS Im and Py rings distinguish AT from GC base pairs because of steric factors involving the bulk of the guanine amine, and the ability of Im to form a hydrogen bond with the amine. Side-by-side Im and Py rings differentiate GC from CG base pairs because of tight steric contacts and sp2 hybridization at the amine nitrogen atom, with the favored conformations being G/Im,Py/C and C/Py,Im/G. Discrimination between AT and TA base pairs may be possible using bulkier rings, such as thiazole to select the A end of the base pair.
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Affiliation(s)
- M L Kopka
- Molecular Biology Institute, University of California at Los Angeles 90095, USA.
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393
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Chikaraishi-Kasuga N, Onoue KI, Osawa Y, Nakahama S, Ohashi Y, Yamaguchi K. Syntheses and Structures of Synthetic Carboxylic Ionophores Containing 2,3-Naphthylene Groups. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.1961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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394
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Chattopadhyay A, Mukherjee S, Rukmini R, Rawat SS, Sudha S. Ionization, partitioning, and dynamics of tryptophan octyl ester: implications for membrane-bound tryptophan residues. Biophys J 1997; 73:839-49. [PMID: 9251800 PMCID: PMC1180980 DOI: 10.1016/s0006-3495(97)78116-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The presence of tryptophan residues as intrinsic fluorophores in most proteins makes them an obvious choice for fluorescence spectroscopic analyses of such proteins. Membrane proteins have been reported to have a significantly higher tryptophan content than soluble proteins. The role of tryptophan residues in the structure and function of membrane proteins has attracted a lot of attention. Tryptophan residues in membrane proteins and peptides are believed to be distributed asymmetrically toward the interfacial region. Tryptophan octyl ester (TOE) is an important model for membrane-bound tryptophan residues. We have characterized this molecule as a fluorescent membrane probe in terms of its ionization, partitioning, and motional characteristics in unilamellar vesicles of dioleoylphosphatidylcholine. The ionization property of this molecule in model membranes has been studied by utilizing its pH-dependent fluorescence characteristics. Analysis of pH-dependent fluorescence intensity and emission maximum shows that deprotonation of the alpha-amino group of TOE occurs with an apparent pKa of approximately 7.5 in the membrane. The fluorescence lifetime of membrane-bound TOE also shows pH dependence. The fluorescence lifetimes of TOE have been interpreted by using the rotamer model for the fluorescence decay of tryptophan. Membrane/water partition coefficients of TOE were measured in both its protonated and deprotonated forms. No appreciable difference was found in its partitioning behavior with ionization. Analysis of fluorescence polarization of TOE as a function of pH showed that there is a decrease in polarization with increasing pH, implying more rotational freedom on deprotonation. This is further supported by pH-dependent red edge excitation shift and the apparent rotational correlation time of membrane-bound TOE. TOE should prove useful in monitoring the organization and dynamics of tryptophan residues incorporated into membranes.
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Affiliation(s)
- A Chattopadhyay
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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395
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Steyaert J. A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:1-11. [PMID: 9249002 DOI: 10.1111/j.1432-1033.1997.t01-1-00001.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
During the last decade, protein engineering has been used to identify the residues that contribute to the ribonuclease-T1-catalyzed transesterification. His40, Glu58 and His92 accelerate the associative nucleophilic displacement at the phosphate atom by the entering 2'-oxygen downstream guanosines in a highly cooperative manner. Glu58, assisted by the protonated His40 imidazole, abstracts a proton from the 2'-oxygen, while His92 protonates the leaving group. Tyr38, Arg77 and Phe100 further stabilize the transition state of the reaction. A functionally independent subsite, including Asn36 and Asn98, contributes to chemical turnover by aligning the substrate relative to the catalytic side chains upon binding of the leaving group. An invariant structural motive, involving residues 42-46, renders ribonuclease T1 guanine specific through a series of intermolar hydrogen bonds. Tyr42 contributes significantly to guanine binding through a parallel face-to-face stacking interaction. Tyr45, often referred to as the lid of the guanine-binding site, does not contribute to the binding of the base.
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Affiliation(s)
- J Steyaert
- Dienst Ultrastruktuur, Vlaams Interuniversitair instituut Biotechnologie, Vrije Universiteit Brussel, Belgium.
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396
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Berna PP, Porath J. Salt-independent adsorption of human serum proteins on cyanocarbon gels. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 693:277-85. [PMID: 9210430 DOI: 10.1016/s0378-4347(97)00030-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Electron donor acceptor gels based on cyanocarbons have been tested for human serum protein adsorption in the absence of salt-promotion by water-structuring salt. This phenomenon was compared with a normal adsorption process in the presence of salt. The tricyanoaminopropene-divinyl sulfone-agarose displayed unusual protein adsorption properties as binding could occur both independently or dependently of the salt-promotion. The absence of hydrophobic or ionic character of the salt-independent interaction suggests an electron donor acceptor adsorption mechanism which is shown, for the first time, to occur independently of salt-promotion in aqueous solution. Study of the protein adsorption specificity showed similar protein selectivity for the fractions adsorbed in both conditions.
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Affiliation(s)
- P P Berna
- Biochemical Separation Centre, Uppsala University, Sweden
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397
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Labeots LA, Weiss MA. Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity. J Mol Biol 1997; 269:113-28. [PMID: 9193004 DOI: 10.1006/jmbi.1997.1026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Electrostatics and hydration of a homeodomain-DNA complex are dissected by chemical modification. Selective neutralization of phosphate charges by methylphosphonate substitution demonstrates the differential importance of short- and long-range electrostatic interactions. Whereas the footprint of direct contacts is in accord with crystal structures, interference is also observed at non-contacted sites. Such sites adjoin a novel interfacial water cavity in the major groove. Non-contacted phosphodiester groups in the cavity are proposed to contribute to long-range ordering of an extended protein-water-DNA interface. Use of isolated S(p) and R(p) methylphosphonate diastereomers demonstrates that interference at this extended interface is stereoselective and charge-independent. Attenuation of protein binding presumably reflects groove-specific reorganization of bound water. Surprisingly, such attenuation can exceed that due to neutralization of a direct phosphate-side-chain salt bridge. These results support the hypothesis that hydration of an interfacial cavity functions as a non-covalent extension of the DNA surface. Stereo-specific interrogation of bound water by chemical synthesis provides a general method to assess the coupling between solvation and DNA recognition.
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Affiliation(s)
- L A Labeots
- Department of Biochemistry and Molecular Biology and Center for Molecular Oncology, The University of Chicago, IL 60637-5419, USA
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398
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Beck B, Clark T, Glen RC. VESPA: A new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(19970430)18:6<744::aid-jcc2>3.0.co;2-s] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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399
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Loverix S, Doumen J, Steyaert J. Additivity of protein-guanine interactions in ribonuclease T1. J Biol Chem 1997; 272:9635-9. [PMID: 9092491 DOI: 10.1074/jbc.272.15.9635] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
It has been established that Tyr-42, Tyr-45, and Glu-46 take part in a structural motif that renders guanine specificity to ribonuclease T1. We report on the impact of Tyr-42, Tyr-45, and Glu-46 substitutions on the guanine specificity of RNase T1. The Y42A and E46A mutations profoundly affect substrate binding. No such effect is observed for Y45A RNase T1. From the kinetics of the Y42A/Y45A and Y42A/E46A double mutants, we conclude that these pairs of residues contribute to guanine specificity in a mutually independent way. From our results, it appears that the energetic contribution of aromatic face-to-face stacking interactions may be significant if polycyclic molecules, such as guanine, are involved.
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Affiliation(s)
- S Loverix
- Dienst Ultrastruktuur, Vlaams Interuniversitair Instituut Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium
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400
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Kobayashi Y, Tsuchiya T. Synthesis of 2"-oxidized derivatives of 5-deoxy-5-epi-5-fluoro-dibekacin and -arbekacin, and study on structure-chemical shift relationships of urethane(or amide)-type NH protons in synthetic intermediates. Carbohydr Res 1997; 298:261-77. [PMID: 9098957 DOI: 10.1016/s0008-6215(96)00318-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Three 2"-modified dibekacin-analogs have been prepared as potential compounds active against resistant bacteria producing 2"-O-phosphotransferases; one is 5-deoxy-5,2"-diepi-5-fluorodibekacin (9) prepared from a suitably protected 2"-O-triflyl derivative through the 2" 3"-cyclic carbamate, and the others are 2"-oxo derivatives (12 and 22, both as the hydrate) of 5-deoxy-5-epi-5-fluoro-dibekacin and -arbekacin prepared through oxidation at C-2" of suitably protected derivatives. Relationships between the t-butoxycarbonyl(= Boc)-NH-shifts of per-N-Boc synthetic intermediates and their structures were studied. It was found that the shifts, measured in pyridine-d5 at 80 degrees C, which spread over a close range (delta 6-7 ppm), are sensitively influenced by nearby and surrounding groups around the BocNH group in respect of electron-withdrawing character, hydrogen bonding (BocNH ... acceptor), and also solvent effects (BocNH ... NC5H5).
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Affiliation(s)
- Y Kobayashi
- Institute of Bioorganic Chemistry, Kawasaki, Japan
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