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Mukherjee M, Ghosh R, Chattopadhyay K, Ghosh S. Stepwise unfolding of a multi-tryptophan protein MPT63 with immunoglobulin-like fold: detection of zone-wise perturbation during guanidine hydrochloride-induced unfolding using phosphorescence spectroscopy. RSC Adv 2016. [DOI: 10.1039/c6ra06545g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The present article highlights the simple inexpensive and rapid technique of phosphorescence spectroscopy at 77 K that reveals the environment of all the four tryptophan residues of a protein MPT63 during guanidine hydrochloride induced unfolding.
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Affiliation(s)
- Manini Mukherjee
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
| | - Ranendu Ghosh
- Structural Biology & Bio-Informatics Division
- Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | - Sanjib Ghosh
- Department of Chemistry
- Presidency University
- Kolkata 700 073
- India
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2
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Suzuki EI, Ishikawa K, Mihara Y, Shimba N, Asano Y. Structural-Based Engineering for Transferases to Improve the Industrial Production of 5′-Nucleotides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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3
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Sardar PS, Maity SS, Ghosh S, Chatterjee J, Maiti TK, Dasgupta S. Characterization of the Tryptophan Residues of Human Placental Ribonuclease Inhibitor and Its Complex with Bovine Pancreatic Ribonuclease A by Steady-State and Time-Resolved Emission Spectroscopy. J Phys Chem B 2006; 110:21349-56. [PMID: 17048964 DOI: 10.1021/jp064832g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human placental ribonuclease inhibitor (hRI) containing six tryptophan (Trp) residues located at positions 19, 261, 263, 318, 375, and 438 and its complex with RNase A have been studied using steady-state and time-resolved fluorescence (298 K) as well as low-temperature phosphorescence (77 K). Two Trp residues in wild-type hRI and also in the protein-protein complex with RNase A are resolved optically. The accessible surface area values of Trp residues in the wild-type hRI and its complex and consideration of inter-Trp energy transfer in the wild-type hRI reveal that one of the Trp residues is Trp19, which is located in a hydrophobic buried region. The other Trp residue is tentatively assigned as Trp375 based on experimental results on wild-type hRI and its complex. This residue in the wild-type hRI is more or less solvent exposed. Both the Trp residues are perturbed slightly on complex formation. Trp19 moves slightly toward a more hydrophobic region, and the environment of Trp375 becomes less solvent exposed. The complex formation also results in a more heterogeneous environment for both the optically resolved Trp residues.
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4
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Hatano KI, Kojima M, Suzuki EI, Tanokura M, Takahashi K. Determination of the NMR structure of Gln25-ribonuclease T1. Biol Chem 2003; 384:1173-83. [PMID: 12974386 DOI: 10.1515/bc.2003.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Ribonuclease (RNase) T1 is a guanyloribonuclease, having two isozymes in nature, Gln25- and Lys25-RNase T1. Between these two isozymes, there is no difference in catalytic activity and three-dimensional structure; however, Lys25-RNase T1 is slightly more stable than Gln25-RNase T1. Recently, it has been suggested that the existence of a salt bridge between Lys25 and Asp29/Glu31 in Lys25-RNase T1 contributes to the stability. To elucidate the effects of the replacement of Lys25 with a Gln on the conformation and microenvironments of RNase T1 in detail, the three-dimensional solution structure of Gln25-RNase T1 was determined by simulated-annealing calculations. As a result, the topology of the overall folding was shown to be very similar to that of the Lys25-isozyme except for some differences. In particular, there were two differences in the property of torsion angles of the two disulfide bonds and the conformations of the residues 11-13, 63-66, and 92-93. With regard to the residues 11-13, the lack of the above-mentioned salt bridge in Gln25-RNase T1 was thought to induce the conformational difference of this segment as compared with the Lys25-isozyme. Furthermore, it was proposed that the perturbation of this segment might transfer to the residues 92-93 via the two disulfide bonds.
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Affiliation(s)
- Ken-ichi Hatano
- Department of Biological Sciences, Faculty of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
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5
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Affiliation(s)
- S Loverix
- Dienst Ultrastructuur, Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, B-1640 Sint-Genesius-Rode, Belgium
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6
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Berezovsky IN, Tumanyan VG, Esipova NG. Representation of amino acid sequences in terms of interaction energy in protein globules. FEBS Lett 1997; 418:43-6. [PMID: 9414092 DOI: 10.1016/s0014-5793(97)01346-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We suggest a new simple approach for comparing the primary structure of proteins and their spatial structure. It relies on the one-to-one correspondence between each residue of the polypeptide chain and the energy of van der Waals interactions between the regions of the native globule flanking this residue. The method obviates the sophisticated geometrical criteria for estimating similarity between spatial structures. Besides, it permits one to analyze structural units of different scale.
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Affiliation(s)
- I N Berezovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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7
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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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8
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Ishikawa K, Suzuki E, Tanokura M, Takahashi K. Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP. Biochemistry 1996; 35:8329-34. [PMID: 8679590 DOI: 10.1021/bi960493d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections > 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization.
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Affiliation(s)
- K Ishikawa
- Central Research Laboratories, Ajinomoto Company, Inc., Kawasaki, Japan
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9
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Elofsson A, Nilsson L. A 1.2 ns Molecular Dynamics Simulation of the Ribonuclease T1−3‘-Guanosine Monophosphate Complex. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952517g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arne Elofsson
- Department of Biochemistry, Arrheniuslaboratoriet, University of Stockholm, S-106 91 Stockholm, Sweden, and Department of Bioscience at NOVUM Center for Structural Biochemistry, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biochemistry, Arrheniuslaboratoriet, University of Stockholm, S-106 91 Stockholm, Sweden, and Department of Bioscience at NOVUM Center for Structural Biochemistry, Karolinska Institutet, S-141 57 Huddinge, Sweden
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10
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Gohda K, Oka K, Tomita K, Hakoshima T. Crystal structure of RNase T1 complexed with the product nucleotide 3‘-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2‘-hydroxyl group of the ribose. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32473-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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Schubert WD, Schluckebier G, Backmann J, Granzin J, Kisker C, Choe HW, Hahn U, Pfeil W, Saenger W. X-ray crystallographic and calorimetric studies of the effects of the mutation Trp59-->Tyr in ribonuclease T1. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 220:527-34. [PMID: 8125111 DOI: 10.1111/j.1432-1033.1994.tb18652.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Two mutants of ribonuclease T1 (RNaseT1), [59-tyrosine]ribonuclease T1 (W59Y) and [45-tryptophan,59-tyrosine]ribonuclease T1 (Y45W/W59Y) possess between 150% and 190% wild-type activity. They have been crystallised as complexes of the inhibitor 2'-guanylic acid and analysed by X-ray diffraction at resolutions of 0.23 nm and 0.24 nm, respectively. The space group for both is monoclinic, P2(1), with two molecules/asymmetric unit, W59Y: a = 4.934 nm, b = 4.820 nm, c = 4.025 nm, beta = 90.29 degrees. Y45W/W59Y: a = 4.915 nm, b = 4.815 nm, c = 4.015 nm, beta = 90.35 degrees. Compared to wild-type RNaseT1 in complex with 2'-guanylic acid (2'GMP) both mutant inhibitor complexes indicate that the replacement of Trp59 by Tyr leads to a 0.04-nm inward shift of the single alpha-helix and to significant differences in the active-site geometry, inhibitor conformation and inhibitor binding. Calorimetric studies of a range of mutants [24-tryptophan]ribonuclease T1 (Y24W), [42-tryptophan]ribonuclease T1 (Y42W), [45-tryptophan]ribonuclease T1 (Y45W), [92-alanine]ribonuclease T1 (H92A) and [92-threonine]ribonuclease T1 (H92T) with and without the further mutation Trp59-->Tyr showed that mutant proteins for which Trp59 is replaced by Tyr exhibit slightly decreased thermal stability.
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Affiliation(s)
- W D Schubert
- Institut für Kristallographie, Freien Universität Berlin, Germany
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Elofsson A, Kulinski T, Rigler R, Nilsson L. Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions. Proteins 1993; 17:161-75. [PMID: 8265564 DOI: 10.1002/prot.340170206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have theoretically and experimentally studied the binding of two different ligands to wild-type ribonuclease T1 (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln. The binding of the natural substrate 3'-GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3'-monophosphate (2AP), and relative free energies of binding of these ligands to the mutant and the wild-type (wt) enzyme have been calculated by free energy perturbation methods. The free energy perturbations predict that the mutant RNT1-Gln-46 binds 2AP better than 3'GMP, in agreement with experiments on dinucleotides. Four free energy perturbations, forming a closed loop, have been performed to allow the detection of systematic errors in the simulation procedure. Because of the larger number of atoms involved, it was necessary to use a much longer simulation time for the change in the protein, i,e., the perturbation from Glu to Gln, than in the perturbation from 3'-GMP to 2AP. Finally the structure of the binding site is analyzed for understanding differences in catalytic speed and binding strength.
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Affiliation(s)
- A Elofsson
- Department of Medical Biophysics, Karolinska Institute, Stockholm, Sweden
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Lam WC, Maki AH, Itoh T, Hakoshima T. Phosphorescence and optically detected magnetic resonance measurements of the 2'AMP and 2'GMP complexes of a mutant ribonuclease T1 (Y45W) in solution: correlation with X-ray crystal structures. Biochemistry 1992; 31:6756-60. [PMID: 1322171 DOI: 10.1021/bi00144a015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphorescence and ODMR measurements have been made on ribonuclease T1 (RNase T1), the mutated enzyme RNase T1 (Y45W), and their complexes with 2'GMP and 2'AMP. It is not possible to observe the phosphorescence of Trp45 in RNase T1 (Y45W). Only that of the naturally occurring Trp59 is seen. The binding of 2'GMP to wild-type RNase T1 produces only a minor red shift in the phosphorescence and no change in the ODMR spectrum of Trp59. However, a new tryptophan 0,0-band is found 8.2 nm to the red of the Trp59 0,0-band in the 2'GMP complex of the mutated RNase T1 (Y45W). Wavelength-selected ODMR measurements reveal that the red-shifted emission induced by 2'GMP binding, assigned to Trp45, occurs from a residue with significantly different zero-field splittings than those of Trp59, a buried residue subject to local polar interactions. The phosphorescence red shift and the zero-field splitting parameters demonstrate that Trp45 is located in a polarizable environment in the 2'GMP complex. In contrast with 2'GMP, binding of 2'AMP to RNase T1 (Y45W) induces no observable phosphorescence emission from Trp45, but leads only to a minor red shift in the phosphorescence origin of Trp59 in both the mutated and wild-type enzyme. The lack of resolved phosphorescence emission from Trp45 in RNase T1 (Y45W) implies that the emission of this residue is quenched in the uncomplexed enzyme. We conclude that local conformational changes that occur upon binding 2'GMP remove quenching residues from the vicinity of Trp45, restoring its luminescence.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- W C Lam
- Chemistry Department, University of California, Davis 95616
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