Characterization of the Electrostatic Perturbation of a Catalytic Site (Cys)-S–/(His)-Im+H Ion-pair in One Type of Serine Proteinase Architecture by Kinetic and Computational Studies on Chemically Mutated Subtilisin Variants

Plou, Francisco J.; Kowlessur, Devanand; Malthouse, J. Paul G.; Mellor, Geoffrey W.; Hartshorn, Michael J.; Pinitglang, Surapong; Patel, H.; Topham, Christopher M.; Thomas, Emrys W.; Verma, Chandra; Brocklehurst, Keith

doi:10.1006/jmbi.1996.0225

Cited by 24 publications

(27 citation statements)

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“…Minimizations were carried out using the steepest descent and adopted-basis Newton-Raphson algorithms [30]. QUANTA and IDRAW were used for visualization and graphics (see [34] for details of the computational techniques).…”

Section: Computer Modellingmentioning

confidence: 99%

Characterization of the hydrolytic activity of a polyclonal catalytic antibody preparation by pH-dependence and chemical modification studies: evidence for the involvement of Tyr and Arg side chains as hydrogen-bond donors

Resmini

Vigna

Simms

et al. 1997

Biochemical Journal

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The hydrolyses of 4-nitrophenyl 4h-(3-aza-2-oxoheptyl)phenyl carbonate and of a new, more soluble, substrate, 4-nitrophenyl 4h-(3-aza-7-hydroxy-2-oxoheptyl)phenyl carbonate, each catalysed by a polyclonal antibody preparation elicited in a sheep by use of an analogous phosphate immunogen, were shown to adhere closely to the Michaelis-Menten equation, in accordance with the growing awareness that polyclonal catalytic antibodies may be much less heterogeneous than had been supposed. The particular value of studies on polyclonal catalytic antibodies is discussed briefly. Both the k cat and k cat \K m values were shown to increase with increase in pH across a pK a of approx. 9. Groupselective chemical modification studies established that the side

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Section: Computer Modellingmentioning

confidence: 99%

Characterization of the hydrolytic activity of a polyclonal catalytic antibody preparation by pH-dependence and chemical modification studies: evidence for the involvement of Tyr and Arg side chains as hydrogen-bond donors

Resmini

Vigna

Simms

et al. 1997

Biochemical Journal

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“…These are important topics of research that in the past few years have been the subject of protein engineering studies involving plant cysteine proteinases [42][43][44] and chemically mutated Ser3 Cys serine proteinases. 45 In this article, we investigated the electrostatic profile in the Cys25/His159 catalytic region of papain, aiming to identify its characteristics and the possible enzymatic regulatory mechanisms in the region where the catalytic residues interact with the ligand and with the active site water molecules. We used a recently developed methodology, the OME (overlapping of multipolar expansions) reassociation method, 46 to obtain a more precise description of the electrostatic field due to the protein matrix charge distribution.…”

Section: Introductionmentioning

confidence: 99%

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

et al. 2003

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We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25 (؊) …His159 (؉) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG3(His159)-ND1 direction; (ii) the electrostatic profile has a saddlepoint character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E SG3 ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236 -253.

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“…An important advance to result from mutation of charged residues, which has implications for enzymes more generally, is the evidence that long-range electrostatic interactions can contribute to stabilization of transition states (e.g., [78][79][80][81]). A complementary approach to structural variation in enzyme structure is the use of natural variants.…”

Section: Serine Proteinasesmentioning

confidence: 99%

“…There is considerable interest also in some of the members of other families such as the human rhinovirus-14 3C proteinase [149] and the human adenovirus proteinase [150], both of which contain Cys-His-Glu catalytic triads, and interleukin-1b-converting enzyme [151], which contains Ser236 instead of a carboxylate analogous to Asp158 of papain and other differences in the electrostatic fields to which the catalytic sites are exposed [81].…”

Section: Cysteine Proteinasesmentioning

confidence: 99%

“…There is considerable variation among members of the papain family, however, in substrate specificity and catalytic-site reactivity [81,[153][154][155][156][157][158], which reveals that this view is correct only for low-resolution aspects of the mechanism, such as the roles of the cysteine and histidine components of the catalytic-site ion pair. The results of detailed mechanistic investigations on papain and some of its natural variants (discussed in [44,45]) have revealed that papain exhibits characteristics at one end of a spectrum of chemical behavior with actinidin at the other, and with caricain and ficin occupying intermediate positions.…”

Section: Cysteine Proteinasesmentioning

confidence: 99%

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Substrate Recognition

Brocklehurst

Gul

Pickersgill

2009

Amino Acids, Peptides and Proteins in Organic Chemistry

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Specific molecular recognition processes by which molecules recognize and discriminate between closely related partners are involved in essentially all aspects of biological function, ranging in complexity from enzyme-inhibitor and enzymesubstrate systems to phenomena such as gene expression, the immune system, and synaptic transmission, and these are important considerations in drug design [1]. This chapter is concerned with general concepts exemplified by a selection of relatively well-defined enzyme-substrate and, by extension, enzyme-inhibitor systems. The original concept of recognition by complementarity in the enzymesubstrate adsorptive (Michaelis) complex was suggested by Emil Fischer in 1894 using his well-known lock-and-key analogy [2]. It is now generally accepted that this has now been superseded by complementarity in the reaction transition state, based on the ideas reported by J.B.S. Haldane [3] in 1930 and elaborated by Linus Pauling [4] in 1946. The catalytic potential of enzymes derives from stabilization in the transition state relative to any stabilization in the Michaelis complex. The latter is anticatalytic in that the free energy expended in stabilizing the adsorptive complex offsets the transition-state stabilization energy (e.g., [5]).Valuable chapters and books on enzyme catalysis and inhibition are available (e.g., [5][6][7][8][9][10][11]) and detailed mechanistic studies on many individual enzymes are described in Sinnot [12]. Macromolecular catalysis includes also catalysis by catalytic antibodies [13] and by synthetic polymers [14], including molecularly imprinted polymers [15]. The contributions of selections of various types of chemical catalysis such as acid-base, nucleophilic, and electrophilic catalysis [5,6,8] are almost always insufficient to account for the high catalytic efficiency of enzymes. A particularly important additional contribution is the entropic advantage that derives from the fact that enzyme catalysis occurs within an enzyme-substrate complex. The complex is essentially a single molecular species and the catalytic act involves one or more unimolecular steps during which there is no loss of translational or rotational entropy

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Characterization of the Electrostatic Perturbation of a Catalytic Site (Cys)-S–/(His)-Im+H Ion-pair in One Type of Serine Proteinase Architecture by Kinetic and Computational Studies on Chemically Mutated Subtilisin Variants

Cited by 24 publications

References 0 publications

Characterization of the hydrolytic activity of a polyclonal catalytic antibody preparation by pH-dependence and chemical modification studies: evidence for the involvement of Tyr and Arg side chains as hydrogen-bond donors

Characterization of the hydrolytic activity of a polyclonal catalytic antibody preparation by pH-dependence and chemical modification studies: evidence for the involvement of Tyr and Arg side chains as hydrogen-bond donors

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair

Substrate Recognition

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