1
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Samaga YBL, Raghunathan S, Priyakumar UD. SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation. J Phys Chem B 2021; 125:10657-10671. [PMID: 34546056 DOI: 10.1021/acs.jpcb.1c04913] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protein sequence space thoroughly are laborious. To this end, many machine learning based methods have been developed to predict thermodynamic stability changes upon mutation. These methods have been evaluated for symmetric consistency by testing with hypothetical reverse mutations. In this work, we propose transitive data augmentation, evaluating transitive consistency with our new Stransitive data set, and a new machine learning based method, the first of its kind, that incorporates both symmetric and transitive properties into the architecture. Our method, called SCONES, is an interpretable neural network that predicts small relative protein stability changes for missense mutations that do not significantly alter the structure. It estimates a residue's contributions toward protein stability (ΔG) in its local structural environment, and the difference between independently predicted contributions of the reference and mutant residues is reported as ΔΔG. We show that this self-consistent machine learning architecture is immune to many common biases in data sets, relies less on data than existing methods, is robust to overfitting, and can explain a substantial portion of the variance in experimental data.
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Affiliation(s)
- Yashas B L Samaga
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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2
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Keikha M, Moghim S, Fazeli H, Nasr-Esfahani B. The Fusion Multistage Synthetic Peptides as the Best Candidates for New Tuberculosis Vaccine. Adv Biomed Res 2018; 7:122. [PMID: 30211135 PMCID: PMC6124223 DOI: 10.4103/abr.abr_116_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Masoud Keikha
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Nasr-Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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3
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Gorai B, Prabhavadhni A, Sivaraman T. Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations. J Biomol Struct Dyn 2014; 33:2037-47. [DOI: 10.1080/07391102.2014.986668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, Olivucci M. Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics. J Phys Chem B 2013; 117:10053-70. [DOI: 10.1021/jp305935t] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark M. Huntress
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Konstantin R. Malley
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Askat E. Jailaubekov
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Mikas Vengris
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
- Faculty of
Physics, Vilnius University, Sauletekio
10 LT10223 Vilnius,
Lithuania
| | - James H. Geiger
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Igor Schapiro
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
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5
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Yang LQ, Sang P, Tao Y, Fu YX, Zhang KQ, Xie YH, Liu SQ. Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. J Biomol Struct Dyn 2013; 32:372-93. [PMID: 23527883 PMCID: PMC3919177 DOI: 10.1080/07391102.2013.770372] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.
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Affiliation(s)
- Li-Quan Yang
- a Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan University , Kunming , 650091 , P.R. China
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6
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Wang XG, Zhang P, Lynch S, Engel PC. Forced evolution ofEscherichia colicells with the ability to effectively utilize non-natural amino acidsl-tert-leucine,l-norleucine and γ-methyl-l-leucine. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.3109/10242422.2010.514047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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7
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Tao Y, Rao ZH, Liu SQ. Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. J Biomol Struct Dyn 2010; 28:143-58. [PMID: 20645649 DOI: 10.1080/073911010010524953] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Because of the significant industrial, agricultural and biotechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (ED) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions but also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation and product release; and the significant displacements in regions opposite the binding groove/pockets are considered to play a role in modulating the dynamics of enzyme-substrate interaction. Our simulation results complement the biochemical and structural studies, highlighting the dynamic mechanism of the functional properties of proteinase K.
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Affiliation(s)
- Yan Tao
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, Yunnan, P R China
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8
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Liu SQ, Tao Y, Meng ZH, Fu YX, Zhang KQ. The effect of calciums on molecular motions of proteinase K. J Mol Model 2010; 17:289-300. [DOI: 10.1007/s00894-010-0724-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/19/2010] [Indexed: 10/19/2022]
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9
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Liu SQ, Meng ZH, Fu YX, Zhang KQ. Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. J Mol Model 2009; 16:17-28. [PMID: 19466463 DOI: 10.1007/s00894-009-0518-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
Abstract
Serine protease proteinase K, a member of the subtilisin family of enzymes, is of significant industrial, agricultural and biotechnological importance. Despite the wealth of structural information about proteinase K provided by static X-ray structures, a full understanding of the enzymatic mechanism requires further insight into the dynamic properties of this enzyme. Molecular dynamics simulations and essential dynamics (ED) analysis were performed to investigate the molecular motions in proteinase K. The results indicate that the internal core of proteinase K is relatively rigid, whereas the surface-exposed loops, most notably the substrate-binding regions, exhibit considerable conformational fluctuations. Further ED analysis reveals that the large concerted motions in the substrate-binding regions cause opening/closing of the substrate-binding pockets, thus supporting the proposed induced-fit mechanism of substrate binding. The distinct electrostatic/hydrogen-bonding interactions between Asp39 and His69 and between His69 and Ser224 within the catalytic triad lead to different thermal motions and orientations of these three catalytic residues, which can be related to their different functional roles in the catalytic process. Statistical analyses of the geometrical/functional properties as well as evolutionary conservation of the glycines in proteinase K-like proteins reveal that glycines may play an important role in determining the folding architecture and structural flexibility of this class of enzymes. Our simulation study complements the biochemical and structural studies and provides new insights into the dynamic structural basis of the functional properties of this class of enzymes.
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Affiliation(s)
- Shu-Qun Liu
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091 Yunnan, P. R. China
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10
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Stabilization of New Imprint Property of Glucose Oxidase in Pure Aqueous Medium by Cross-Linked-Imprinting Approach. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/978-1-59745-053-9_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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12
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Fitzpatrick PA, Ringe D, Klibanov AM. Computer-assisted modeling of subtilisin enantioselectivity in organic solvents. Biotechnol Bioeng 2004; 40:735-42. [DOI: 10.1002/bit.260400613] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Martin JR, Mulder FA, Karimi-Nejad Y, van der Zwan J, Mariani M, Schipper D, Boelens R. The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site. Structure 1997; 5:521-32. [PMID: 9115441 DOI: 10.1016/s0969-2126(97)00208-6] [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: 02/04/2023]
Abstract
BACKGROUND Research on high-alkaline proteases, such as serine protease PB92, has been largely inspired by their industrial application as protein-degrading components of washing powders. Serine protease PB92 is a member of the subtilase family of enzymes, which has been extensively studied. These studies have included exhaustive protein engineering investigations and X-ray crystallography, in order to provide insight into the mechanism and specificity of enzyme catalysis. Distortions have been observed in the substrate-binding region of subtilisin crystal structures, due to crystal contacts. In addition, the structural variability in the substrate-binding region of subtilisins is often attributed to flexibility. It was hoped that the solution structure of this enzyme would provide further details about the conformation of this key region and give new insights into the functional properties of these enzymes. RESULTS The three-dimensional solution structure of the 269-residue (27 kDa) serine protease PB92 has been determined using distance and dihedral angle constraints derived from triple-resonance NMR data. The solution structure is represented by a family of 18 conformers which overlay onto the average structure with backbone and all-heavy-atom root mean square deviations (for the main body of the molecule) of 0.88 and 1.21 A, respectively. The family of structures contains a number of regions of relatively high conformational heterogeneity, including various segments that are involved in the formation of the substrate-binding site. The presence of flexibility within these segments has been established from NMR relaxation parameters and measurements of amide proton exchange rates. CONCLUSIONS The solution structure of the serine protease PB92 presents a well defined global fold which is rigid with the exception of a restricted number of sites. Among the limited number of residues involved in significant internal mobility are those of two pockets, termed S1 and S4, within the substrate-binding site. The presence of flexibility within the binding site supports the proposed induced fit mechanism of substrate binding.
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Affiliation(s)
- J R Martin
- Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH, Utrecht, The Netherlands
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14
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Häring D, Herderich M, Schüler E, Withopf B, Schreier P. Efficient and enantioselective catalysis by the semisynthetic peroxidase seleno-subtilisin. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0957-4166(97)00068-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Abstract
We describe methods for displaying the protease trypsin and the macromolecular protease inhibitor ecotin on the surface of filamentous phage. Our strategy for selecting variant ecotins against target proteases is also described. We believe that the two proteins that have been displayed serve as ideal models for studying molecular recognition in detail. The ability to search efficiently through a large number of variant proteins for desired properties using phage display technology and the in vitro selection methods described opens a new avenue for studying protein-ligand interactions, as well as creating proteins with novel functions.
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Affiliation(s)
- C I Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA
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16
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Maurer KH, Markgraf M, Goddette D. Substrate specificity of natural variants and genetically engineered intermediates of Bacillus lentus alkaline proteases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1996; 379:243-56. [PMID: 8796329 DOI: 10.1007/978-1-4613-0319-0_26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Three natural variants of subtilisin lentus could be differentiated by their amino acid sequence and their specific activity with low molecular weight peptide substrates of the type sAAPFpNA. The variants had amino acid exchanges in five, respective six positions of their amino acid sequence, four of which are located in the substrate loop of the enzyme (positions 92 - 102). Variants of one type of highly alkaline subtilisin (subtilisin 309) were made by site directed mutagenesis, each containing one of the corresponding amino acid exchanges. These intermediate forms were tested for activity, pH-dependence and substrate specificity. The changes in substrate affinity were relatively small for substrates with different amino acids as P1 residue. The differences in activity on peptide-substrates could be related primarily to a single amino acid substitution in the S4 substrate binding pocket in position 102. With substrate variations in the P3 amino acid residue, changes in k(cat) and K(m) revealed the importance of the charged amino acid exchanged between subtilisin 309 and BLAP. By these experiments an interaction of amino acid position 101 and the P3 residue of the substrate could be demonstrated. The substitution of two differently charged amino acids in the substrate binding region resulted in an unchanged pH-profile of the natural enzyme. With the single exchange intermediates differences in the pH-profile could be found, depending on the substrate tested: a characteristic change was observed with casein as substrate, no such change occurred with hemoglobin.
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17
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Zamocky M, Herzog C, Nykyri LM, Koller F. Site-directed mutagenesis of the lower parts of the major substrate channel of yeast catalase A leads to highly increased peroxidatic activity. FEBS Lett 1995; 367:241-5. [PMID: 7607315 DOI: 10.1016/0014-5793(95)00568-t] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Five single replacement mutants of catalase A from Saccharomyces cerevisiae were prepared (F148V, F149V, F156V, F159V, and V111A). The exchanges were expected to relieve steric constraints in the lowest part of the major substrate channel. The overall stability of the isolated enzymes is unaffected by the respective amino acid exchanges, but some modifications lead to decreased protohaem binding. All isolated mutants (most pronounced the V111A-species) show decreased catalatic and markedly increased peroxidatic activity, both with aliphatic and aromatic substrates. These effects can in part be explained by steric effects, but also reveal destabilisation of compound I.
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Affiliation(s)
- M Zamocky
- Institute of Biochemistry and Molecular Cell Biology, University of Vienna, Austria
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18
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Yamagata Y, Isshiki K, Ichishima E. Subtilisin Sendai from alkalophilic Bacillus sp.: molecular and enzymatic properties of the enzyme and molecular cloning and characterization of the gene, aprS. Enzyme Microb Technol 1995; 17:653-63. [PMID: 7605625 DOI: 10.1016/0141-0229(94)00109-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We purified a new extracellular serine proteinase (designated subtilisin Sendai) from the culture broth of alkalophilic Bacillus sp. G-825-6, and its properties were characterized. Its optimum pH was at 10.0, when succinyl-L-leucyl-L-leucyl-L-valyl-L-tyrosyl-4-methylcoumaryl-7-amide (Suc-Leu-Leu-Val-Tyr-MCA) was used as a substrate. The substrate specificity of subtilisin Sendai was determined with oxidized insulin B-chain and fluorogenic peptidyl-MCA substrates. The isoelectric point of subtilisin Sendai was over 11.0. The molecular mass of the enzyme was estimated as 28,000 using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The circular dichroism spectrum of the enzyme was measured, and we discuss the relationship between the secondary structure of the enzyme and alkaline stability at pH 12 in comparison with that of subtilisin NAT. The structural gene (aprS) was cloned and sequenced. The deduced amino acid sequence for the mature protein (269 amino acids) was preceded by a putative signal sequence of 27 residues and a putative pro-sequence of 86 amino acids. The homology of the primary structure for 13 subtilisins was compared. The catalytic triad (Asp32, His64, and Ser221 with the numbering of subtilisin BPN') and the amino acid sequences near these amino acid residues were well conserved. As a special feature, it was observed that there was an extensive number of negatively charged amino acids in the pro-region of subtilisin Sendai and alkaline subtilisins. This was different from those of subtilisin from neutrophiles.
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Affiliation(s)
- Y Yamagata
- Department of Applied Biological Chemistry, Faculty of Agriculture, Tohoku University, Sendai, Japan
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19
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Fogh RH, Schipper D, Boelens R, Kaptein R. Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus. JOURNAL OF BIOMOLECULAR NMR 1995; 5:259-270. [PMID: 7787423 DOI: 10.1007/bf00211753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The 1H, 13C and 15N NMR resonances of serine protease PB92 have been assigned using 3D triple-resonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CHn carbons, all amide (NH and NH2) nitrogens and 99.2% of the amide and CHn protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405-411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.
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Affiliation(s)
- R H Fogh
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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20
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Abstract
The degree of oligomerization (or in some cases aggregation) often determines the physiological half-life and uptake rate of a protein preparation. High-resolution crystal structures of insulin and other pharmacologically interesting proteins have aided in the design of mutants with altered quaternary structure and physiological uptake rates. Analysis of the contacts between natural oligomers and protein complexes can indicate sequences that may enhance protein oligomerization. These sequences can be altered to produce monomeric protein.
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Affiliation(s)
- C H Schein
- Swiss Institute for Alternatives to Animal Testing (SIAT), Zürich
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21
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Villafane R, Fleming A, Haase-Pettingell C. Isolation of suppressors of temperature-sensitive folding mutations. J Bacteriol 1994; 176:137-42. [PMID: 8282689 PMCID: PMC205024 DOI: 10.1128/jb.176.1.137-142.1994] [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: 01/29/2023] Open
Abstract
Mutations in the tailspike gene (gene 9) of Salmonella typhimurium phage P22 have been used to identify amino acid interactions during the folding of a polypeptide chain. Since temperature-sensitive folding (tsf) mutations cause folding defects in the P22 tailspike polypeptide chain, it is likely that mutants derived from these and correcting the original tsf defects (second-site intragenic suppressors) identify interactions during the folding pathway. We report the isolation and identification of second-site revertants to tsf mutants.
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Affiliation(s)
- R Villafane
- Department of Microbiology, University of Tennessee, Knoxville 37996
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22
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Fogh RH, Schipper D, Boelens R, Kaptein R. (1)H, (13)C and (15)N NMR backbone assignments of the 269-residue serine protease PB92 from Bacillus alcalophilus. JOURNAL OF BIOMOLECULAR NMR 1994; 4:123-128. [PMID: 22911160 DOI: 10.1007/bf00178340] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/1993] [Accepted: 10/26/1993] [Indexed: 06/01/2023]
Abstract
The (1)H, (13)C and (15)N NMR resonances of the backbone of serine protease PB92 have been assigned. This 269-residue protein is one of the largest monomeric proteins assigned so far. The amount and quality of information available suggest that even larger proteins could be assigned with present methods. Measured chemical shifts show excellent agreement with the secondary structure.
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Affiliation(s)
- R H Fogh
- Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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23
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Godzik A, Kolinski A, Skolnick J. De novo and inverse folding predictions of protein structure and dynamics. J Comput Aided Mol Des 1993; 7:397-438. [PMID: 8229093 DOI: 10.1007/bf02337559] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized structures is discussed, and for eight-membered beta-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of supersecondary structure including beta-hairpins, helical hairpins and alpha/beta/alpha fragments. Then, we describe a very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3-4 A from native. Furthermore, the de novo algorithms can assess the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorithm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem.
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Affiliation(s)
- A Godzik
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
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24
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Shopes B. A genetically engineered human IgG with limited flexibility fully initiates cytolysis via complement. Mol Immunol 1993; 30:603-9. [PMID: 8487779 DOI: 10.1016/0161-5890(93)90035-a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A causal link between antigen induced conformational change and functional activity has been previously suggested for the triggering of immunoglobulin effector functions. To test this hypothesis an immunoglobulin with greatly restricted Fab flexibility has been created by site-directed mutagenesis. Serine119, a residue at the elbow in the first heavy chain constant domain of a mouse-human chimeric immunoglobulin, was replaced by cysteine119. The resulting mutant immunoglobulin had an additional intramolecular disulfide bond connecting the two heavy chains. This newly introduced covalent bond between antigen binding arms gave rise to a compact 'tethered' conformation which displayed lowered segmental flexibility as determined by nanosecond fluorescence depolarization anisotropy. However, the ability of this tethered immunoglobulin to initiate lysis of target cells via the complement cascade was unimpaired. Therefore, it is likely that allosteric or distortive mechanisms of conformational change induced complement activation which require unhindered 'twist' and/or 'waggle' motions of Fab are untenable.
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Affiliation(s)
- B Shopes
- Department of Cell Biology, Stanford School of Medicine, CA 94305
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25
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Albert DE, Douglas MB, Hintz MA, Youngen CS, Keyes MH. Semisynthetic fluorohydrolases prepared by chemical modification of ribonuclease. Enzyme Microb Technol 1992; 14:885-92. [PMID: 1368989 DOI: 10.1016/0141-0229(92)90051-o] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A process for conformational modification of protein, which we have previously reported, was investigated as a means of generating fluorohydrolase activity in bovine ribonuclease (RNase). The resulting modified RNase had catalytic activity that depended upon the chosen modifier. Bovine pancreatic ribonuclease, modified by addition of hexamethylphosphoramide (HMPA) at pH 3, was derivatized with diimidates of chain lengths from C1 to C8. The derivative with the highest activity was obtained when RNase was crosslinked with dimethyl pimelimidate (C5). This derivative, which was active over a pH range of 6.5 to 8.0 with an optimum pH of 7.4, hydrolyzed phenylmethylsulfonylfluoride (PMSF) and the potent acetylcholinesterase inhibitor, diisopropyl phosphorofluoridate (DFP). The mean fluorohydrolase activity for four preparations using dimethyl pimelimidate was 0.8 +/- 0.2 U mg-1. Gel filtration on G-75 Sephadex and SDS-polyacrylamide gel electrophoresis showed components having a molecular weight of 13,000 and 27,000, with activity restricted to the 27,000 molecular weight fraction. After gel filtration, the specific activity was 9.1 +/- 2.4 U mg-1, resulting in a molecular activity of 125 min-1. The mechanism of this unique transformation of RNase into a fluorohydrolase is not known, nor has the location of the active site been determined.
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26
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Loetscher P, Pratt G, Rechsteiner M. The C terminus of mouse ornithine decarboxylase confers rapid degradation on dihydrofolate reductase. Support for the pest hypothesis. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)99150-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Mazzella LJ, Pazhanisamy S, Pratt RF. Evidence from a mutant beta-lactamase for the mechanism of beta-lactamase-catalysed depsipeptide aminolysis. Biochem J 1991; 274 ( Pt 3):855-9. [PMID: 2012612 PMCID: PMC1149989 DOI: 10.1042/bj2740855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Ser-70----Gly mutant of the TEM-1 beta-lactamase, where the active-site serine hydroxy group has been lost, does not catalyse the hydrolysis of either benzylpenicillin or N-(phenylacetyl)glycyl depsipeptides. This is as would be expected for a double-displacement mechanism where the Ser-70 becomes acylated at an intermediate stage. Further, however, the mutant enzyme, unlike the wild-type, does not catalyse aminolysis of depsipeptides by D-phenylalanine. If the active site is not structurally disrupted by the mutation, this result shows that Ser-70 is necessary for the aminolysis reaction and implies that this reaction, like the hydrolysis, proceeds by way of an acyl-(serine)-enzyme intermediate. Although physical evidence suggests that the mutant enzyme does not have a structure in solution identical with that of the wild-type, the mutant does still bind beta-lactam substrates. The latter result suggests sufficient conservation of the active-site structure for the major conclusion above to hold.
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Affiliation(s)
- L J Mazzella
- Department of Chemistry, Wesleyan University, Middletown, CT 06457
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28
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Abstract
The conserved topological structure observed in various molecular families such as globins or cytochromes c allows structural equivalencing of residues in every homologous structure and defines in a coherent way a global alignment in each sequence family. A search was performed for equivalent residue pairs in various topological families that were buried in protein cores or exposed at the protein surface and that had mutated but maintained similar unmutated environments. Amino acid residues with atoms in contact with the mutated residue pairs defined the environment. Matrices of preferred amino acid exchanges were then constructed and preferred or avoided amino acid substitutions deduced. Given the conserved atomic neighborhoods, such natural in vivo substitutions are subject to similar constrains as point mutations performed in site-directed mutagenesis experiments. The exchange matrices should provide guidelines for "safe" amino acid substitutions least likely to disturb the protein structure, either locally or in its overall folding pathway, and most likely to allow probing the structural and functional significance of the substituted site.
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Affiliation(s)
- D Bordo
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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29
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Kristjánsson MM, Kinsella JE. Protein and enzyme stability: structural, thermodynamic, and experimental aspects. ADVANCES IN FOOD AND NUTRITION RESEARCH 1991; 35:237-316. [PMID: 1930884 DOI: 10.1016/s1043-4526(08)60066-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M M Kristjánsson
- Marine Biotechnology Center, Technical University of Denmark, Lyngby
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30
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31
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Abstract
This review deals with ways of stabilizing proteins against aggregation and with methods to determine, predict, and increase solubility. Solvent additives (osmolytes) that stabilize proteins are listed with a description of their effects on proteins and on the solvation properties of water. Special attention is given to areas where solubility limitations pose major problems, as in the preparation of highly concentrated solutions of recombinant proteins for structural determination with NMR and X-ray crystallography, refolding of inclusion body proteins, studies of membrane protein dynamics, and in the formulation of proteins for pharmaceutical use. Structural factors relating to solubility and possibilities for protein engineering are analyzed.
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Affiliation(s)
- C H Schein
- Department of Organic Chemistry, CHN E56, Swiss Federal Institute of Technology, Zürich
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32
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Bordo D, Argos P. Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures. J Mol Biol 1990; 211:975-88. [PMID: 2313703 DOI: 10.1016/0022-2836(90)90087-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The amino acid sequences of ten globin chain tertiary structures were aligned and structurally equivalenced by spatial superposition of main-chain C alpha atoms. A search was then performed for structurally equivalent residue pairs that were buried in the protein core and that had mutated but maintained similar unmutated environments. Residues with atoms in contact with such central residue pairs define their environments. Such examples of point mutations would represent in vivo site-directed mutagenesis as would be observed in evolution. A search for mutated but exposed equivalent central residues was also performed. The constraints placed on the characteristics of the mutated residues (e.g., side-chain volume, polarity, radius of gyration) allow suggestions for the evolutionary modes of protein core and surface development as well as residue substitution guidelines to maintain structural stability in protein engineering and design.
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Affiliation(s)
- D Bordo
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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33
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Demchenko AP, Chinarov VA. Stochastic dynamics and function of proteins. Modelling the membrane ionic channels. J Mol Liq 1990. [DOI: 10.1016/0167-7322(90)80086-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Olsen DB, Eckstein F. High-efficiency oligonucleotide-directed plasmid mutagenesis. Proc Natl Acad Sci U S A 1990; 87:1451-5. [PMID: 2154748 PMCID: PMC53493 DOI: 10.1073/pnas.87.4.1451] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A number of single- and double-base substitutions have been introduced into either the polylinker region or the lacZ gene in the plasmid vector pUC19. The efficiencies of these changes upon transfection of TG-1 bacterial cells were generally 70-80%. A strategy has been devised by which the wild-type DNA can be selectively destroyed. It is primarily based on the resistance of phosphorothioate internucleotide linkages to some restriction enzymes. A mismatch oligonucleotide is introduced into a gapped region and the gap is filled using three deoxynucleoside 5'-triphosphates and one deoxynucleoside 5'-[alpha-thio]triphosphate. Reaction with a restriction enzyme that is unable to hydrolyze phosphorothioates ensures that the DNA containing the mismatch oligonucleotide is only nicked. Concomitantly, the DNA that does not contain the desired mutation is linearized. Subsequent reactions with an exonuclease and DNA polymerase I yield mutant homoduplex DNA for transfection.
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Affiliation(s)
- D B Olsen
- Max-Planck Institut für Experimentelle Medizin, Abteilung Chemie, Göttingen, Federal Republic of Germany
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35
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Carey PR, Tonge PJ. Chemistry of enzyme–substrate complexes revealed by resonance Raman spectroscopy. Chem Soc Rev 1990. [DOI: 10.1039/cs9901900293] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Hermes JD, Blacklow SC, Knowles JR. Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme. Proc Natl Acad Sci U S A 1990; 87:696-700. [PMID: 1967829 PMCID: PMC53332 DOI: 10.1073/pnas.87.2.696] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How easy is it to improve the catalytic power of an enzyme? To address this question, the gene encoding a sluggish mutant triose-phosphate isomerase (D-glyceraldehyde-3-phosphate ketol-isomerase, EC 5.3.1.1) has been subjected to random mutagenesis over its whole length by using "spiked" oligonucleotide primers. Transformation of an isomerase-minus strain of Escherichia coli was followed by selection of those colonies harboring an enzyme of higher catalytic potency. Six amino acid changes in the Glu-165----Asp mutant of triosephosphate isomerase improve the specific catalytic activity of this enzyme (from 1.3-fold to 19-fold). The suppressor sites are scattered across the sequence (at positions 10, 96, 97, 167, and 233), but each of them is very close to the active site. These experiments show both that there are relatively few single amino acid changes that increase the catalytic potency of this enzyme and that all of these improvements derive from alterations that are in, or very close to, the active site.
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Affiliation(s)
- J D Hermes
- Department of Chemistry, Harvard University, Cambridge, MA 02138
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37
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Docherty K, Rhodes CJ, Taylor NA, Shennan KIJ, Hutton JC. Proinsulin endopeptidase substrate specificities defined by site-directed mutagenesis of proinsulin. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)51468-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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38
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Náray-Szabó G, Nagy J, Bérces A. Rational design in genetic engineering: dream or reality? A priori predictions for thrombin and ribonuclease a mutants. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0166-1280(89)85068-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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40
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Mutter M, Vuilleumier S. Ein chemischer Weg zu neuen Proteinen – Templat-assoziierte synthetische Proteine (TASP). Angew Chem Int Ed Engl 1989. [DOI: 10.1002/ange.19891010504] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Mutter M, Vuilleumier S. A Chemical Approach to Protein Design?Template-Assembled Synthetic Proteins (TASP). ACTA ACUST UNITED AC 1989. [DOI: 10.1002/anie.198905353] [Citation(s) in RCA: 328] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Borriss R, Olsen O, Thomsen KK, von Wettstein D. Hybrid bacillus endo-(1-3,1-4)-beta-glucanases: construction of recombinant genes and molecular properties of the gene products. CARLSBERG RESEARCH COMMUNICATIONS 1989; 54:41-54. [PMID: 2673278 DOI: 10.1007/bf02907584] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hybrid beta-glucanase genes were constructed by the reciprocal exchange of the two halves of the isolated beta-glucanase genes from Bacillus amyloliquefaciens and B. macerans. The beta-glucanase hybrid enzyme 1 (H1) contains the 107 amino-terminal residues of mature B. amyloliquefaciens beta-glucanase and the 107 carboxyl-terminal amino acid residues of B. macerans beta-glucanase. The reciprocal beta-glucanase hybrid enzyme 2 (H2) consists of the 105 amino-terminal residues from the B. macerans enzyme and the carboxyl-terminal 107 amino acids from B. amyloliquefaciens. The biochemical properties of the two hybrid enzymes differ significantly from each other as well as from both parental beta-glucanases. Hybrid beta-glucanase H1 exhibits increased thermostability in comparison to other beta-glucanases, especially in an acidic environment. This hybrid enzyme has maximum activity between pH 5.6 and 6.6, whereas the pH-optimum for enzymatic activity of B. amyloliquefaciens beta-glucanase was found to be at pH 6 to 7 and for B. macerans at pH 6.0 to 7.5. Hybrid enzyme 1 being more heat stable than both parental enzymes represents a case of intragenic heterosis. Hybrid beta-glucanase 2 (H2) was found to be more thermolabile than the naturally occurring beta-glucanases it was derived from and the pH-optimum for enzymatic activity was determined to be between pH 7 and pH 8.
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Affiliation(s)
- R Borriss
- Sektion Nahrungsgüterwirtschaft und Lebensmitteltechnologie, Bereich Mikrobiologie, Humboldt-Universität Berlin, DDR
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43
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44
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Scrutton NS, Berry A, Perham RN. Engineering of an intersubunit disulphide bridge in glutathione reductase from Escherichia coli. FEBS Lett 1988; 241:46-50. [PMID: 3058515 DOI: 10.1016/0014-5793(88)81028-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
By site-directed mutagenesis, Thr-75 was converted to Cys-75 in the glutathione reductase (EC 1.6.4.2) of Escherichia coli. This led to the spontaneous formation of an intersubunit disulphide bridge across the 2-fold axis of the dimeric enzyme. The disulphide bridge had no deleterious effect on the catalytic activity, but nor did it increase the thermal stability of the enzyme, possibly because of local conformational flexibility on the dimer interface. The T75C mutant, like the wild-type enzyme, was inactivated by NADPH, proving that this inactivation cannot be due to simple dissociation of the dimer.
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Affiliation(s)
- N S Scrutton
- Department of Biochemistry, University of Cambridge, England
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45
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Brocklehurst K, Brocklehurst SM, Kowlessur D, O'Driscoll M, Patel G, Salih E, Templeton W, Thomas E, Topham CM, Willenbrock F. Supracrystallographic resolution of interactions contributing to enzyme catalysis by use of natural structural variants and reactivity-probe kinetics. Biochem J 1988; 256:543-58. [PMID: 3223929 PMCID: PMC1135444 DOI: 10.1042/bj2560543] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
1. The influence on the reactivities of the catalytic sites of papain (EC 3.4.22.2) and actinidin (3.4.22.14) of providing for interactions involving the S1-S2 intersubsite regions of the enzymes was evaluated by using as a series of thiol-specific two-hydronic-state reactivity probes: n-propyl 2-pyridyl disulphide (I) (a 'featureless' probe), 2-(acetamido)ethyl 2'-pyridyl disulphide (II) (containing a P1-P2 amide bond), 2-(acetoxy)ethyl 2'-pyridyl disulphide (III) [the ester analogue of probe (II)] and 2-carboxyethyl 2'-pyridyl disulphide N-methylamide (IV) [the retroamide analogue of probe (II)]. Syntheses of compounds (I), (III) and (IV) are reported. 2. The reactivities of the two enzymes towards the four reactivity probes (I)-(IV) and also that of papain towards 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide (VII) (containing both a P1-P2 amide bond and an L-phenylalanyl side chain as an occupant for the S2 subsite), in up to four hydronic (previously called protonic) states, were evaluated by analysis of pH-dependent stopped-flow kinetic data (for the release of pyridine-2-thione) by using an eight-parameter rate equation [described in the Appendix: Brocklehurst & Brocklehurst (1988) Biochem. J. 256, 556-558] to provide pH-independent rate constants and macroscopic pKa values. The analysis reveals the various ways in which the two enzymes respond very differently to the binding of ligands in the S1-S2 intersubsite regions despite the virtually superimposable crystal structures in these regions of the molecules. 3. Particularly striking differences between the behaviour of papain and that of actinidin are that (a) only papain responds to the presence of a P1-P2 amide bond in the probe such that a rate maximum at pH 6-7 is produced in the pH-k profile in place of the rate minimum, (b) only in the papain reactions does the pKa value of the alkaline limb of the pH-k profile change from 9.5 to approx. 8.2 [the value characteristic of a pH-(kcat./Km) profile] when the probe contains a P1-P2 amide bond, (c) only papain reactivity is affected by two positively co-operative hydronic dissociations with pKI congruent to pKII congruent to 4 and (d) modulation of the reactivity of the common -S(-)-ImH+ catalytic-site ion-pair (Cys-25/His-159 in papain and Cys-25/His-162 in actinidin) by hydronic dissociation with pKa approx. 5 is more marked and occurs more generally in reactions of actinidin than is the case for papain reactions.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- K Brocklehurst
- Department of Biochemistry, Medical College of St. Bartholomew's Hospital, University of London, U.K
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46
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Jimenez-Flores R, Richardson T. Genetic Engineering of the Caseins to Modify the Behavior of Milk During Processing: A Review. J Dairy Sci 1988. [DOI: 10.3168/jds.s0022-0302(88)79857-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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47
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48
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Tian GC, Sanders CR, Kishi F, Nakazawa A, Tsai MD. Mechanism of adenylate kinase. Histidine-36 is not directly involved in catalysis, but protects cysteine-25 and stabilizes the tertiary structure. Biochemistry 1988; 27:5544-52. [PMID: 2846042 DOI: 10.1021/bi00415a024] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Several previous reports on muscle adenylate kinase (AK) have suggested that histidine-36 (His-36) is located in the binding site of adenosine 5'-triphosphate (ATP) and is involved in catalysis. We have tested the role of His-36 using site-specific mutagenesis on chicken muscle AK expressed in Escherichia coli. Three mutant proteins (H36Q, H36N, and H36G) were obtained by substituting His-36 with glutamine, asparagine, and glycine, respectively. Steady-state kinetic studies showed that the mutants have similar kinetic properties to those of the wild-type (WT) AK, which suggested that His-36 is not directly involved in catalysis. However, His-36 is likely to interact with or protect cysteine-25 (Cys-25) on the basis of the following evidence: The crystal structure of porcine muscle AK revealed a close proximity between His-36 and Cys-25; the mutants were unstable during purification (the order of stability was WT greater than H36Q greater than H36N greater than H36G); the H36G mutant readily dimerized; the sulfhydryl groups of mutants became more reactive (WT less than H36Q less than H36N) toward 5,5'-dithiobis(2-nitrobenzoic acid). Furthermore, His-36 was found to stabilize the tertiary structure of AK on the basis of guanidine hydrochloride induced denaturation studies, which showed that the conformational stability decreases in the order WT greater than H36Q greater than H36N.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G C Tian
- Department of Chemistry, Ohio State University, Columbus 43210
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49
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Mozhaev VV, Berezin IV, Martinek K. Structure-stability relationship in proteins: fundamental tasks and strategy for the development of stabilized enzyme catalysts for biotechnology. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1988; 23:235-81. [PMID: 3069328 DOI: 10.3109/10409238809088225] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The problem of relationships between the protein structure and its stability comprises two major questions. First, how to elucidate the peculiarities of the protein structure responsible for its stability. Second, knowing the general molecular basis of protein stability, how to change the structure of a given protein in order to increase its stability. This review is an attempt to show the modern state of the first (fundamental) and the second (applied) aspects of the problem.
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Affiliation(s)
- V V Mozhaev
- Chemistry Department, Moscow State University, U.S.S.R
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50
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Madgwick PJ, Waley SG. beta-lactamase I from Bacillus cereus. Structure and site-directed mutagenesis. Biochem J 1987; 248:657-62. [PMID: 3124817 PMCID: PMC1148599 DOI: 10.1042/bj2480657] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The sequence of the gene for beta-lactamase I from Bacillus cereus 569/H has been redetermined. Oligonucleotide-directed mutagenesis has been carried out, and the effects of the changes on the ampicillin-resistance of Escherichia coli TG1 expressing the mutant genes have been studied. Lysine-73, close to the active-site serine-70 and a highly-conserved residue, has been converted into arginine. This change had a large effect on activity, but did not abolish it. An even larger effect was found in the mutant in which glutamate-166 had been converted into glutamine; this had little or no activity. On the other hand, the conversion of glutamate-168 into aspartate gave fully active enzyme. Glutamate-166 is an invariant residue, but glutamate-168 is not. Alanine-123 has been replaced by cysteine, to give active enzyme; this change forms part of the plan to introduce a disulphide bond into the enzyme.
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Affiliation(s)
- P J Madgwick
- Sir William Dunn School of Pathology, University of Oxford, U.K
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