Conformational adaptability in enzymes

Ratcheting synthesis

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.

Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations

The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this study, atomistic simulations are employed to identify the modes of essential dynamics that define the conformational response of the enzyme to ligand binding and unbinding. The binding modes and the binding affinities of the products to the DapE enzyme are estimated from the MM-PBSA method, and the residues contributing to the ligand binding are identified. Various structural analyses and the principal component analysis of the molecular dynamics trajectories reveal that the removal of products from the active site causes a significant change in the overall enzyme structure. Both Cartesian and dihedral principal component analyses are used to characterize the structural changes in terms of domain unfolding and domain twisting motions. In the most dominant mode, that is, the domain unfolding motion, the two catalytic domains move away from the two dimerization domains of the dimeric enzyme, representing a closed-to-open conformational change. The conformational changes are initiated by the coordinated movement of three loops (Asp75-Pro82, Gly240-Asn244, and Thr347-Glu353) that trigger a domain-level movement. From multiple short trajectories, the time constant associated with the domain opening motion is estimated as 43.6 ns. Physiologically, this close-to-open conformational change is essential for the regeneration of the initial state of the enzyme for the subsequent cycle of catalytic action and provides the apo enzyme enough flexibility for efficient substrate binding.

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (K_d), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.

Challenges in enzyme mechanism and energetics

Since the discovery of enzymes as biological catalysts, study of their enormous catalytic power and exquisite specificity has been central to biochemistry. Nevertheless, there is no universally accepted comprehensive description. Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an absolute partitioning of catalytic contributions into independent and energetically additive components. Site-directed mutagenesis has emerged as an enormously powerful approach to probe enzymatic catalysis, illuminating many basic features of enzyme function and behavior. The emphasis of site-directed mutagenesis on the role of individual residues has also, inadvertently, limited experimental and conceptual attention to the fundamentally cooperative nature of enzyme function and energetics. The first part of this review highlights the structural and functional interconnectivity central to enzymatic catalysis. In the second part we ask: What are the features of enzymes that distinguish them from simple chemical catalysts? The answers are presented in conceptual models that, while simplified, help illustrate the vast amount known about how enzymes achieve catalysis. In the last section, we highlight the molecular and energetic questions that remain for future investigation and describe experimental approaches that will be necessary to answer these questions. The promise of advancing and integrating cutting edge conceptual, experimental, and computational tools brings mechanistic enzymology to a new era, one poised for novel fundamental insights into biological catalysis.

Binding patterns and kinetics of RNase a interaction with RNA

Kinetics and binding studies of RNase A and its natural polymeric substrate (RNA), as well as the natural mixture of free 3'-ribonucleotides, were performed by difference spectrophotometry. The obtained kinetic saturation curve, with an anomalous nonhyperbolic shape and a distinct transition point, showed the interchange between the two conformational forms of the enzyme. This occurred in a narrow range of substrate concentration. At low substrate concentration, in spite of the existence of one catalytic cleft, RNase A behaves as a cooperative system, perhaps due to the interactions among the four cooperative binding subsites in the active cleft. At high substrate concentration, the conformational change did occur and was accompanied by a decrease in cooperativity and increment of the catalytic constant. The multiphasic shape of the binding curve, which, in the presence of the enzyme, produced 3'-ribonucleotides (as the ligand molecules), shows four binding subsites. The first three subsites are specific for the attachment of phosphate, ribose, and base moieties belonging to the first bound 3'-ribonucleotide in the direction of 3'-phosphate --> ribose --> base-5'. The fourth subsite relates to the second phosphate group of the second bound 3'-ribonucleotide. The binding direction also converts to 5'-phosphate --> ribose --> base-3' for the ribonucleotide monomers in the RNA structure.

Synergistic binding of inhibitors to the protease from HIV type 1

Inhibition of the protease in HIV is a potentially useful approach for the treatment of AIDS. In the course of evaluating inhibitors of the HIV-1 protease, we observed a strong synergism between certain inhibitors that might be expected to bind to different sites in this enzyme. The binding affinity of carbobenzyloxyisoleucinylphenylalaninol, for example, is increased 125-fold in the presence of carbobenzyloxyglutaminylisoamylamide. These synergistic effects between inhibitors have specific structural requirements that correlate well with the known substrate preference of the enzyme. The modular basis for this phenomenon remains to be elucidated but it could involve substrate-induced conformational change as part of the reaction mechanism. Similar effects have been reported previously for several zinc proteases. Thus this work extends the observation to a different class of enzymes and suggests that the phenomenon might be widespread.

Conformational changes induced in herpes simplex virus DNA polymerase upon DNA binding

Herpesvirus DNA polymerases are prototypes for alpha-like DNA polymerases and important targets for antiherpesvirus drugs. We have investigated changes in the catalytic subunit of herpes simplex virus DNA polymerase following DNA binding by using the techniques of endogeneous fluorescence quenching and limited proteolysis. The fluorescence studies revealed a reduction in the rate of quenching by acrylamide in the presence of DNA without changes in the wavelength of the emission peak or in the lifetime of the fluorophore, consistent with the possibility of conformational changes. Strikingly, the proteolysis studies revealed that binding to a variety of natural and synthetic DNA and RNA molecules induced the appearance of a new cleavage site for trypsin near residue 1060 of the protein and increased cleavage by trypsin near the center of the protein. The extent of these cleavages correlated with the affinity of the polymerase for these ligands. These data provide strong evidence that binding to nucleic acid polymers induces substantial localized conformational changes in the polymerase. The locations of enhanced tryptic cleavage near sites implicated in substrate recognition and interaction with a processivity factor suggest that the conformational changes are important for catalysis and processivity of this prototype alpha-like DNA polymerase. Inhibition of these changes may provide a mechanism for antiherpesvirus drugs.

The Molecular Basis of β-Lactamase Catalysis and Inhibition

The β-lactamases catalyze the hydrolysis of the lactam bond in β-lactams, thus rendering the β-lactam ineffective as an antibiotic. The increasing spread of resistance to β-lactam antibiotics is largely due to this class of enzyme. Mechanistically these enzymes appear to be related to the transpeptidases and carboxypeptidases involved in the synthesis of the bacterial cell wall. Interest in the basic mechanism of action of the β-lactamases has been spurred by the potential for mechanism-based drug design. The past seven years have seen a significant increase in our knowledge of the catalysis and inhibition of the β-lactamases. The presence of an essential, conserved, serine residue which participates in the formation of a covalent acyl-enzyme intermediate in catalysis, inhibition and inactivation by β-lactams has been established. Unfortunately, few additional details regarding the catalytic mechanism are well established. A generalized reaction pathway can be formulated for most β-lactam inhibitors (reversible or irreversible). This scheme involves partitioning of the initially-formed acyl-enzyme by three pathways: 1) hydrolysis leading to turnover, 2) transient inhibition probably involving formation of an imine or enamine acyl-enzyme, or possibly involving a substantial conformational change in some cases, and 3) imine formation followed by additional covalent modification of the enzyme leading to irreversible inactivation. The flux through each of these pathways varies with the nature of the "substrate" and the particular β-lactamase.

Ligand-mediated conformational changes in wheat-germ aspartate transcarbamoylase indicated by proteolytic susceptibility

Ligand-mediated effects on the inactivation of pure wheat-germ aspartate transcarbamoylase by trypsin were examined. Inactivation was apparently first-order in all cases, and the effects of ligand concentration on the pseudo-first-order rate constant, k, were studied. Increase in k (labilization) was effected by carbamoyl phosphate, phosphate and the putative transition-state analogue, N-phosphonoacetyl-L-aspartate. Decrease in k (protection) was effected by the end-product inhibitor, UMP, and by the ligand pairs aspartate/phosphate and succinate/carbamoyl phosphate, but not by aspartate or succinate alone up to 10 mM. Except for protection by the latter ligand pairs, all other ligand-mediated effects were also observed on inactivation of the enzyme by Pronase and chymotrypsin. Ligand-mediated effects on the fragmentation of the polypeptide chain by trypsin were examined electrophoretically. Slight labilization of the chain was observed in the presence of carbamoyl phosphate, phosphate and N-phosphonoacetyl-L-aspartate. An extensive protection by UMP was observed, which apparently included all trypsin-sensitive peptide bonds. No significant effect by the ligand pair succinate/carbamoyl phosphate was noted. It is concluded from these observations that UMP triggers an extensive, probably co-operative, transition to a proteinase-resistant conformation, and that carbamoyl phosphate similarly triggers a transition to an alternative, proteinase-sensitive, conformation. These antagonistic conformational changes may account for the regulatory kinetic effects reported elsewhere [Yon (1984) Biochem. J. 221, 281-287]. The protective effect by the ligand pairs aspartate/phosphate and succinate/carbamoyl phosphate, which operates only against trypsin, is concluded to be due to local shielding of essential lysine or arginine residues in the aspartate-binding pocket of the active site, to which aspartate (or its analogue, succinate) can only bind as part of a ternary complex.

The chymotrypsin-catalysed activation of bovine liver glutamate dehydrogenase

1. Ox liver glutamate dehydrogenase is activated by bovine pancreatic alpha-chymotrypsin, but the extent of activation is dependent on the age of the dehydrogenase preparation. 2. The degree of activation is constant and the pseudo-first-order rate constant of activation is directly proportional to the concentration of proteinase used. 3. Commercial preparations of alpha-chymotrypsin differ in their ability to produce a secondary inactivation phase, and this was shown to be due to low tryptic contamination. The 'superactive' form of glutamate dehydrogenase has an increased sensitivity to tryptic inactivation as compared with the native enzyme. 4. Analysis of the activation by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis revealed that the subunit molecular weight of 'superactive' glutamate dehydrogenase differs by less than 5% from that of the native subunit.

Interaction of the pBR 322-coded RTEM beta-lactamase with substrates. Evidence for specific conformational transitions

The rate of inactivation of RTEM-1 beta-lactamase by Pronase is accelerated by class A ('resistant') penicillins. Other substrates (class S penicillin and cephalosporins) protect against the inactivation. Cefoxitin, a semi-synthetic cephamycin, induces a more extensive, hysteretic response. In its presence the enzyme is inactivated by trypsin as well as by Pronase.

Cyclic AMP-dependent protein kinase I: cyclic nucleotide binding, structural changes, and release of the catalytic subunits

Type I cyclic AMP (cAMP)-dependent protein kinase is composed of a dimeric regulatory subunit (R(2)) and two catalytic subunits (C subunits). The R(2) dimer binds four cAMP molecules to release the two C subunits. To characterize the cAMP binding sites and elucidate their role in the release of the C subunits, the R(2) dimer has been studied by equilibrium methods. The cAMP titration of R(2) was monitored by endogenous tryptophan fluorescence, and the results suggest one class of binding sites. The titration plot is monotonic for saturation of four sites per R(2). A similar titration monitored by near-UV circular dichroic changes exhibited profound changes in the region of the (1)L(b) tyrosine and (1)L(a) and (1)L(b) tryptophan transitions; a plot of these data also showed a linear monotonic response. Thus, the fluorescence and circular dichroic changes show that cAMP binding to R(2) induces a conformational or structural change. The one apparent class of binding sites implies that all binding sites are characterized by similar K(d) values or by K(d) values much less than the receptor concentration. The reactivity of the cysteine sulfhydryl groups with 5,5'-dithiobis(2-nitrobenzoic acid) showed that saturation with cAMP indirectly protects one sulfhydryl group per R monomer. Analysis of cAMP activation of the holoenzyme, detected by phosphotransferase assays, showed that saturation of both cAMP binding sites per R monomer is necessary to effect the release of the C subunit. By using a fluorescent analog of cAMP, 1,N(6)-etheno-cyclic AMP (epsilon cAMP), the (epsilon cAMP)(4).R(2) complex was titrated with C subunit, causing the release of epsilon cAMP. The titration showed that the release of epsilon cAMP was a positive cooperative process; its Hill plot had a slope of 2.6 and the K(a1) and K(an) values obtained by extrapolation were 2.1 x 10(7) M(-1) and 5.0 x 10(8) M(-1), respectively. The calculated DeltaDeltaG for first and last site coupling was 1.9 kcal/mol (1 cal = 4.18 J) of holoenzyme.

Cross-linking preserves conformational changes induced in penicillinase by its substrates

Exopenicillinase of Bacillus cereus 569/H was cross-linked with toluene 2,4-diisocyanate in the presence of cephalothin, cloxacillin or no substrate. The derivatives show significant differences in susceptibility to inactivation by heat, urea, iodination or proteolysis. Such differences can be predicted from the contrasting effects of these substrates on the conformation of the enzyme.

Substrate-induced deactivation of penicillinases. Studies of beta-lactamase I by hydrogen exchange

The conformational motility of beta-lactamase I from Bacillus cereus was studied by hydrogen exhange. The time course of the isotopic replacement of peptide hydrogen atoms was followed by 'exchange-in' or 'exchange-out' experiments. Many of the substrates for this enzyme that have o-substituted aromatic or heterocyclic side chains (e.g. methicillin or cloxacillin) are known to effect a decrease in enzymic activity ('substrate-induced deactivation'). There was a marked discontinuity in the exchange-out curve when methicillin or cloxacillin was diffused into the enzyme solution. About one-half of the hydrogen atoms that were probed were affected by the presence of these substrates, and the change in the reactivity of the hydrogen atoms was also large. Substrates that do not bring about deactivation (benzylpenicillin and cephalosporin C) do not affect the hydrogen exchange, nor do reversible competitive inhibitors such as the penicilloic acid or penilloic acid. On the other hand, Zn2+ ions do affect the hydrogen exchange; their effect is similar to that of methicillin or cloxacillin.

Theories of enzyme specificity and their application to proteases and aminoacyl-transfer RNA synthetases

The question of enzyme specificity which is a corollary of the phenomenon of biological recognition is reviewed. The following theories are outlined briefly: non-productive binding, induced fit, transition state binding, the general strain theory and the kinetic proofreading hypothesis. Data on proteolytic enzymes and aminoacyl-tRNA synthetases are discussed in the light of predictions made by the various theories. The specificity of inhibitor and substrate binding to chymotrypsin and subtilisins is revealed at the sub-molecular level as an example of binding specificity. Kinetic specificity is experimentally distinguished from binding specificity. Conformational adaptability of enzyme and substrate, which is crucial in some theories, is documented by data on aminoacyl-tRNA synthetases. Expected and observed specificity of tRNA charging is discussed with regard to a theoretical limit of specificity. Additional means seem necessary beside those contained in the isolated enzyme-substrate system to account for the high specificity of most synthetases. In conclusion, we have arrived at quite good explanations for moderate specificity such as is displayed by many proteases, but there are still ample difficulties in the understanding of highly specific enzyme reactions.

Determination of the execution points of mutations in the nuclear replication cycle of Aspergillus nidulans

Cultures of nuclear replication cycle mutants of Aspergillus nidulans were transferred to the nonpermissive temperature, and the fraction of nuclei still able to reach mitosis was determined. For the determinations, benomyl [methyl-1(butylcarbomoyl)benzimidazolecarbamate] was added to trap nuclei in mitosis, and these were detected by staining with aceto-orcein. The assumptions and controls required to relate the experimentally determined fractions to the points where a mutation blocks the nuclear cycle are discussed. Nine genetically distinct mutants were tested. Two of these were blocked early in the cycle, two in the middle, and five close to, or during, mitosis.

Acquisition of substrate-specific parameters during the catalytic reaction of penicillinase

The progress of the catalytic reaction of penicillinase (EC 3.5.2.6; penicillin amido-beta-lactamhydrolase) depends on the structure of the side-chain in derivatives of 6-aminopenicillanic acid (the parent substrate). Side-chains of one class promote the rate of the reaction and cause no deviation from the linear kinetics observed with the parent compound. By contrast, side-chains of the other class induce a time-dependent, reversible change in the parameters of the catalytic reaction. The rate decelerates considerably and then becomes constant; the decrease in kcat is accompanied by a corresponding decrease in Km. The initial parameters of the biphasic reaction, determined by stopped-flow spectrophotometry, approach those of the unsubstituted 6-aminopenicillanic acid. The final parameters, which are specific for each derivative, are not acquired when the native conformation of the enzyme is stabilized by homologous antibodies.

An allosteric model for ribonuclease

Data from two assay systems show that the kinetics of the hydrolysis of cytidine 2':3'-cyclic monophosphate by bovine pancreatic RNAase (ribonuclease) is not consistent with conventional models. An allosteric model involving a substrate-dependent change in the equilibrium between two enzyme conformations is proposed. Such a model gives rise to a calculated curve of velocity versus substrate concentration which fits the experimental data. The model is also consistent with the results of an examination of the tryptic digestion of RNAase. Substrate analogues are able to protect RNAase against hydrolysis by trypsin and the percentage of RNAase activity which remains after digestion increases sigmoidally as the analogue concentration is increased. The model also explains the pattern seen in the Km values quoted in the literature and is consistent with strong physical evidence for a ligand-induced conformational change for RNAase reported in the literature.