1
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Blankenship E, Vukoti K, Miyagi M, Lodowski DT. Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:833-40. [PMID: 24598752 PMCID: PMC3949523 DOI: 10.1107/s1399004713033658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 05/20/2024]
Abstract
With more than 500 crystal structures determined, serine proteases make up greater than one-third of all proteases structurally examined to date, making them among the best biochemically and structurally characterized enzymes. Despite the numerous crystallographic and biochemical studies of trypsin and related serine proteases, there are still considerable shortcomings in the understanding of their catalytic mechanism. Streptomyces erythraeus trypsin (SET) does not exhibit autolysis and crystallizes readily at physiological pH; hence, it is well suited for structural studies aimed at extending the understanding of the catalytic mechanism of serine proteases. While X-ray crystallographic structures of this enzyme have been reported, no coordinates have ever been made available in the Protein Data Bank. Based on this, and observations on the extreme stability and unique properties of this particular trypsin, it was decided to crystallize it and determine its structure. Here, the first sub-angstrom resolution structure of an unmodified, unliganded trypsin crystallized at physiological pH is reported. Detailed structural analysis reveals the geometry and structural rigidity of the catalytic triad in the unoccupied active site and comparison to related serine proteases provides a context for interpretation of biochemical studies of catalytic mechanism and activity.
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Affiliation(s)
- Elise Blankenship
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krishna Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Opthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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2
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Masuda Y, Nitanai Y, Mizutani R, Noguchi S. Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated. Proteins 2012; 81:526-30. [PMID: 23161653 DOI: 10.1002/prot.24206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 11/06/2022]
Abstract
The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation.
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Affiliation(s)
- Yosuke Masuda
- Nuclear, Biological and Chemical Detection Technology Section, Human Oriented Systems Division, Advanced Defense Technology Center, Technical Research and Development Institute, Ministry of Defense, Meguro, Tokyo 153-8630, Japan.
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3
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Kaushik S, Mohanty D, Surolia A. Molecular Dynamics Simulations onPars Intercerebralis MajorPeptide-C (PMP-C) Reveal the Role of Glycosylation and Disulfide Bonds in its Enhanced Structural Stability and Function. J Biomol Struct Dyn 2012; 29:905-20. [DOI: 10.1080/073911012010525026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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4
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Zhou Y, Wang S, Zhang Y. Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. J Phys Chem B 2010; 114:8817-25. [PMID: 20550161 DOI: 10.1021/jp104258d] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.
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Affiliation(s)
- Yanzi Zhou
- Department of Chemistry, New York University, New York, New York 10003, USA
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5
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Khan MN. Can a Typical Protein Assist the Rate of its Own Aqueous Cleavage? PROGRESS IN REACTION KINETICS AND MECHANISM 2010. [DOI: 10.3184/146867810x12700573609126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A recent finding of a large rate enhancement in the intramolecular secondary amide group-assisted cleavage of an adjacent tertiary amide bond predicts the possibility of the cleavage of the peptide bond of a protein through a similar reaction mechanism. Based upon enzymatic partial model reactions, the usual proton-switch mechanism has been suggested for the acylation step of the chymotrypsin–catalysed cleavage of the peptide bond which does not favour a His57-shift mechanism - an essential component of the classical charge relay mechanism. Also, the proton-switch mechanism does not necessarily require the two proton-transfer of the classical charge relay mechanism. The unique structural feature of the imidazole moiety of His57 is concluded to be essential in decreasing the rate of collapse of the proposed reactive tetrahedral intermediate back to the reactants. The proposed intramolecular intimate ion-pair formation between anionic Asp102 and cationic His57 is attributed to the energetically preferred location of the proton at Nδ1 of the imidazole moiety of His57. Thus, the analysis described in this review does not favour the necessary requirements of a two proton-transfer and His57-shift as proposed in the classical charge relay mechanism as well as the relatively recently proposed His57-flip mechanism.
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Affiliation(s)
- Mohammad Niyaz Khan
- Department of Chemistry, University of Malaya, Faculty of Science, 50603 Kuala Lumpur, Malaysia
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6
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Structure of West Nile Virus NS3 Protease: Ligand Stabilization of the Catalytic Conformation. J Mol Biol 2009; 385:1568-77. [DOI: 10.1016/j.jmb.2008.11.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Revised: 11/14/2008] [Accepted: 11/18/2008] [Indexed: 11/20/2022]
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7
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Richards WG. From diatomics to drugs and dividends. J Mol Graph Model 2007; 26:596-601. [PMID: 17482855 DOI: 10.1016/j.jmgm.2007.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 04/03/2007] [Accepted: 04/03/2007] [Indexed: 11/17/2022]
Abstract
The path from diatomic molecule spectroscopy to molecular modelling and drug discovery is described, along with aspects of the commercialisation of research. It is a history tightly coupled with the advances in computers over the past 50 years, but with a future full of opportunity.
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8
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Brauer ABE, McBride JD, Kelly G, Matthews SJ, Leatherbarrow RJ. Resisting degradation by human elastase: commonality of design features shared by 'canonical' plant and bacterial macrocyclic protease inhibitor scaffolds. Bioorg Med Chem 2007; 15:4618-28. [PMID: 17470393 DOI: 10.1016/j.bmc.2007.03.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 03/26/2007] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
A previously unexplained difference in the resistance to enzymatic hydrolysis of 11-mer Bowman-Birk-type inhibitors of human leukocyte elastase that differ in P1 is found to correlate with the strength of a particular intramolecular hydrogen bond within the inhibitor. This transannular hydrogen bond stabilizes the side chain of the conserved P2 Thr in a 'canonical' +60 degrees -rotamer chi(1) conformation and thereby directs it for a close interaction with the enzyme's catalytic His. As the implications of this NMR analysis are neither limited to this macrocyclic scaffold derived from plant proteins nor to a particular serine protease, we present a unified analysis with inhibitory bacterial depsipeptides of 7-12 residues in length that share key design features for which we propose communal functional explanations.
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Affiliation(s)
- Arnd B E Brauer
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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9
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Solá RJ, Griebenow K. Influence of modulated structural dynamics on the kinetics of alpha-chymotrypsin catalysis. Insights through chemical glycosylation, molecular dynamics and domain motion analysis. FEBS J 2006; 273:5303-19. [PMID: 17076704 DOI: 10.1111/j.1742-4658.2006.05524.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although the chemical nature of the catalytic mechanism of the serine protease alpha-chymotrypsin (alpha-CT) is largely understood, the influence of the enzyme's structural dynamics on its catalysis remains uncertain. Here we investigate whether alpha-CT's structural dynamics directly influence the kinetics of enzyme catalysis. Chemical glycosylation [Solá RJ & Griebenow K (2006) FEBS Lett 580, 1685-1690] was used to generate a series of glycosylated alpha-CT conjugates with reduced structural dynamics, as determined from amide hydrogen/deuterium exchange kinetics (k(HX)). Determination of their catalytic behavior (K(S), k(2), and k(3)) for the hydrolysis of N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (Suc-Ala-Ala-Pro-Phe-pNA) revealed decreased kinetics for the catalytic steps (k(2) and k(3)) without affecting substrate binding (K(S)) at increasing glycosylation levels. Statistical correlation analysis between the catalytic (DeltaG( not equal)k(i)) and structurally dynamic (DeltaG(HX)) parameters determined revealed that the enzyme acylation and deacylation steps are directly influenced by the changes in protein structural dynamics. Molecular modelling of the alpha-CT glycoconjugates coupled with molecular dynamics simulations and domain motion analysis employing the Gaussian network model revealed structural insights into the relation between the protein's surface glycosylation, the resulting structural dynamic changes, and the influence of these on the enzyme's collective dynamics and catalytic residues. The experimental and theoretical results presented here not only provide fundamental insights concerning the influence of glycosylation on the protein biophysical properties but also support the hypothesis that for alpha-CT the global structural dynamics directly influence the kinetics of enzyme catalysis via mechanochemical coupling between domain motions and active site chemical groups.
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Affiliation(s)
- Ricardo J Solá
- Laboratory for Applied Biochemistry and Biotechnology, Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931
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10
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Liu B, Schofield CJ, Wilmouth RC. Structural analyses on intermediates in serine protease catalysis. J Biol Chem 2006; 281:24024-35. [PMID: 16754679 DOI: 10.1074/jbc.m600495200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the subject of many studies, detailed structural information on aspects of the catalytic cycle of serine proteases is lacking. Crystallographic analyses were performed in which an acyl-enzyme complex, formed from elastase and a peptide, was reacted with a series of nucleophilic dipeptides. Multiple analyses led to electron density maps consistent with the formation of a tetrahedral species. In certain cases, apparent peptide bond formation at the active site was observed, and the electron density maps suggested production of a cis-amide rather than a trans-amide. Evidence for a cis-amide configuration was also observed in the noncovalent complex between elastase and an alpha1-antitrypsin-derived tetrapeptide. Although there are caveats on the relevance of the crystallographic data to solution catalysis, the results enable detailed proposals for the pathway of the acylation step to be made. At least in some cases, it is proposed that the alcohol of Ser-195 may preferentially attack the carbonyl of the cis-amide form of the substrate, in a stereoelectronically favored manner, to give a tetrahedral oxyanion intermediate, which undergoes N-inversion and/or C-N bond rotation to enable protonation of the leaving group nitrogen. The mechanistic proposals may have consequences for protease inhibition, in particular for the design of high energy intermediate analogues.
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Affiliation(s)
- Bin Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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11
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Radisky ES, Lee JM, Lu CJK, Koshland DE. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. Proc Natl Acad Sci U S A 2006; 103:6835-40. [PMID: 16636277 PMCID: PMC1458980 DOI: 10.1073/pnas.0601910103] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction.
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Affiliation(s)
- Evette S. Radisky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Justin M. Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Chia-Jung Karen Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Daniel E. Koshland
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
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12
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Barends TRM, Polderman-Tijmes JJ, Jekel PA, Williams C, Wybenga G, Janssen DB, Dijkstra BW. Acetobacter turbidans alpha-amino acid ester hydrolase: how a single mutation improves an antibiotic-producing enzyme. J Biol Chem 2005; 281:5804-10. [PMID: 16377627 DOI: 10.1074/jbc.m511187200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The alpha-amino acid ester hydrolase (AEH) from Acetobacter turbidans is a bacterial enzyme catalyzing the hydrolysis and synthesis of beta-lactam antibiotics. The crystal structures of the native enzyme, both unliganded and in complex with the hydrolysis product D-phenylglycine are reported, as well as the structures of an inactive mutant (S205A) complexed with the substrate ampicillin, and an active site mutant (Y206A) with an increased tendency to catalyze antibiotic production rather than hydrolysis. The structure of the native enzyme shows an acyl binding pocket, in which D-phenylglycine binds, and an additional space that is large enough to accommodate the beta-lactam moiety of an antibiotic. In the S205A mutant, ampicillin binds in this pocket in a non-productive manner, making extensive contacts with the side chain of Tyr(112), which also participates in oxyanion hole formation. In the Y206A mutant, the Tyr(112) side chain has moved with its hydroxyl group toward the catalytic serine. Because this changes the properties of the beta-lactam binding site, this could explain the increased beta-lactam transferase activity of this mutant.
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Affiliation(s)
- Thomas R M Barends
- Laboratories of Biophysical Chemistry and Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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13
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Haddad KC, Sudmeier JL, Bachovchin DA, Bachovchin WW. alpha-lytic protease can exist in two separately stable conformations with different His57 mobilities and catalytic activities. Proc Natl Acad Sci U S A 2005; 102:1006-11. [PMID: 15657134 PMCID: PMC545854 DOI: 10.1073/pnas.0409279102] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
alpha-Lytic protease is a bacterial serine protease widely studied as a model system of enzyme catalysis. Here we report that lyophilization induces a structural change in the enzyme that is not reversed by redissolution in water. The structural change reduces the mobility of the active-site histidine residue and the catalytic activity of the enzyme. The application of mild pressure to solutions of the altered enzyme reverses the lyophilization-induced structural change and restores the mobility of the histidine residue and the enzyme's catalytic activity. This effect of lyophilization permits a unique opportunity for investigating the relationship between histidine ring dynamics and catalytic activity. The results demonstrate that His57 in resting enzymes is more mobile than previously thought, especially when protonated. The histidine motion and its correlation to enzyme activity lend support to the reaction-driven ring flip hypothesis.
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Affiliation(s)
- Kristin Coffman Haddad
- Department of Biochemistry, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA
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14
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Topf M, Richards WG. Theoretical studies on the deacylation step of serine protease catalysis in the gas phase, in solution, and in elastase. J Am Chem Soc 2004; 126:14631-41. [PMID: 15521783 DOI: 10.1021/ja047010a] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The deacylation step of serine protease catalysis is studied using DFT and ab initio QM/MM calculations combined with MD/umbrella sampling calculations. Free energies of the entire reaction are calculated in the gas phase, in a continuum solvent, and in the enzyme elastase. The calculations show that a concerted mechanism in the gas phase is replaced by a stepwise mechanism when solvent effects or an acetate ion are added to the reference system, with the tetrahedral intermediate being a shallow minimum on the free energy surface. In the enzyme, the tetrahedral intermediate is a relatively stable species ( approximately 7 kcal/mol lower in energy than the transition state), mainly due to the electrostatic effects of the oxyanion hole and Asp102. It is formed in the first step of the reaction, as a result of a proton transfer from the nucleophilic water to His57 and of an attack of the remaining hydroxyl on the ester carbonyl. This is the rate-determining step of the reaction, which requires approximately 22 kcal/mol for activation, approximately 5 kcal/mol less than the reference reaction in water. In the second stage of the reaction, only small energy barriers are detected to facilitate the proton transfer from His57 to Ser195 and the breakdown of the tetrahedral intermediate. Those are attributed mainly to a movement of Ser195 and to a rotation of the His57 side chain. During the rotation, the imidazolium ion is stabilized by a strong H-bond with Asp102, and the C(epsilon)(1)-H...O H-bond with Ser214 is replaced by one with Thr213, suggesting that a "ring-flip mechanism" is not necessary as a driving force for the reaction. The movements of His57 and Ser195 are highly correlated with rearrangements of the binding site, suggesting that product release may be implicated in the deacylation process.
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Affiliation(s)
- Maya Topf
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QZ, United Kingdom.
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15
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Fuentes-Prior P, Salvesen G. The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem J 2004; 384:201-32. [PMID: 15450003 PMCID: PMC1134104 DOI: 10.1042/bj20041142] [Citation(s) in RCA: 609] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Revised: 08/31/2004] [Accepted: 09/27/2004] [Indexed: 02/07/2023]
Abstract
The death morphology commonly known as apoptosis results from a post-translational pathway driven largely by specific limited proteolysis. In the last decade the structural basis for apoptosis regulation has moved from nothing to 'quite good', and we now know the fundamental structures of examples from the initiator phase, the pre-mitochondrial regulator phase, the executioner phase, inhibitors and their antagonists, and even the structures of some substrates. The field is as well advanced as the best known of proteolytic pathways, the coagulation cascade. Fundamentally new mechanisms in protease regulation have been disclosed. Structural evidence suggests that caspases have an unusual catalytic mechanism, and that they are activated by apparently unrelated events, depending on which position in the apoptotic pathway they occupy. Some naturally occurring caspase inhibitors have adopted classic inhibition strategies, but other have revealed completely novel mechanisms. All of the structural and mechanistic information can, and is, being applied to drive therapeutic strategies to combat overactivation of apoptosis in degenerative disease, and underactivation in neoplasia. We present a comprehensive review of the caspases, their regulators and inhibitors from a structural and mechanistic point of view, and with an aim to consolidate the many threads that define the rapid growth of this field.
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Key Words
- apoptosis
- caspase
- inhibitor
- inhibitor of apoptosis protein (iap)
- protease
- zymogen
- alps, autoimmune lymphoproliferative syndrome
- apaf-1, apoptotic protease activating factor-1
- asc/pycard, apoptosis-associated speck-like protein containing a card/pyd- and card-containing molecule
- bir, baculoviral iap repeat
- cad, caspase-activated dnase
- card, caspase-recruitment domain
- carp, caspase-associated ring protein
- ced, cell death-defective
- clarp, caspase-like apoptosis-regulatory protein
- cradd/raidd, caspase-2 and ripk1 domain-containing adaptor with death domain/rip-associated protein with a death domain
- crma, cytokine response modifier a
- dd, death domain
- ded, death effector domain
- dff, dna fragmentation factor
- diablo, direct iap-binding protein with low pi
- diap1, drosophila inhibitor of apoptosis 1
- disc, death-inducing signalling complex
- dronc, drosophila nedd2-like caspase
- fadd, fas (tnfrsf6)-associated via death domain
- flice, fadd-like ice
- flip, flice inhibitory protein
- iap, inhibitor of apoptosis protein
- ibm, iap binding motif
- icad, inhibitor of cad
- ice, interleukin-1β-converting enzyme
- ipaf/clan, ice-protease-activating factor/card, lrr and nacht-containing protein
- lrr, leucine-rich repeat
- nacht, ntpase-domain named after naip, ciita, het-e and tp1
- nalp1, nacht, lrr and pyrin domain containing 1
- nbd, nucleotide-binding domain
- nf-κb, nuclear factor-κb
- nod, nucleotide-binding and oligomerization domain-containing protein
- parp, poly(adp-ribose) polymerase
- pidd, p53-induced protein with a death domain
- rick/cardiak, rip-like interacting clarp kinase/card-containing ice-associated kinase
- ring, really interesting new gene
- rip, receptor-interacting protein
- serpin, serine protease inhibitor
- smac, second mitochondrial activator of caspases
- tfpi, tissue factor pathway inhibitor
- tlr, toll-like receptor
- tnf, tumour necrosis factor
- tradd, tnfrsf1a-associated via death domain
- traf, tnf receptor-associated factor
- trail, tnf-related apoptosis-inducing ligand
- xiap/birc4, x-linked iap/baculoviral iap repeat-containing 4
- p1, p2, …pn and p1′, p2′, …pm′ designate the side chains in substrates and inhibitors in the n- and c-terminal direction respectively from the p1–p1′ scissile peptide bond
- s1, s2, …sn and s1′, s2′, …sm′ refer to the cognate pockets on the protease that accept these side chains [1]
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Affiliation(s)
- Pablo Fuentes-Prior
- *Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D82152, Planegg-Martinsried, Germany and Cardiovascular Research Center, Sant Antoni Ma. Claret 167, 08025 Barcelona, Spain
| | - Guy S. Salvesen
- †The Program in Apoptosis and Cell Death Research, Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, U.S.A
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16
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Gleeson MP, Hillier IH, Burton NA. Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design. Org Biomol Chem 2004; 2:2275-80. [PMID: 15305206 DOI: 10.1039/b402399d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.
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Affiliation(s)
- M Paul Gleeson
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, United Kingdom M13 9PL
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17
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Aertgeerts K, Ye S, Tennant MG, Kraus ML, Rogers J, Sang BC, Skene RJ, Webb DR, Prasad GS. Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation. Protein Sci 2004; 13:412-21. [PMID: 14718659 PMCID: PMC2286704 DOI: 10.1110/ps.03460604] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dipeptidyl peptidase IV (DPPIV) is a member of the prolyl oligopeptidase family of serine proteases. DPPIV removes dipeptides from the N terminus of substrates, including many chemokines, neuropeptides, and peptide hormones. Specific inhibition of DPPIV is being investigated in human trials for the treatment of type II diabetes. To understand better the molecular determinants that underlie enzyme catalysis and substrate specificity, we report the crystal structures of DPPIV in the free form and in complex with the first 10 residues of the physiological substrate, Neuropeptide Y (residues 1-10; tNPY). The crystal structure of the free form of the enzyme reveals two potential channels through which substrates could access the active site-a so-called propeller opening, and side opening. The crystal structure of the DPPIV/tNPY complex suggests that bioactive peptides utilize the side opening unique to DPPIV to access the active site. Other structural features in the active site such as the presence of a Glu motif, a well-defined hydrophobic S1 subsite, and minimal long-range interactions explain the substrate recognition and binding properties of DPPIV. Moreover, in the DPPIV/tNPY complex structure, the peptide is not cleaved but trapped in a tetrahedral intermediate that occurs during catalysis. Conformational changes of S630 and H740 between DPPIV in its free form and in complex with tNPY were observed and contribute to the stabilization of the tetrahedral intermediate. Our results facilitate the design of potent, selective small molecule inhibitors of DPPIV that may yield compounds for the development of novel drugs to treat type II diabetes.
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Schmidt A, Jelsch C, Ostergaard P, Rypniewski W, Lamzin VS. Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis. J Biol Chem 2003; 278:43357-62. [PMID: 12937176 DOI: 10.1074/jbc.m306944200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.
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Affiliation(s)
- Andrea Schmidt
- European Molecular Biology Laboratory (EMBL) Hamburg c/o DESY, D-22607 Hamburg, Germany.
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HOWARD BRIANJ, GRANT GUYH. (William) Graham Richards. Mol Phys 2003. [DOI: 10.1080/00268970310001605741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Brauer ABE, Nievo M, McBride JD, Leatherbarrow RJ. The structural basis of a conserved P2 threonine in canonical serine proteinase inhibitors. J Biomol Struct Dyn 2003; 20:645-56. [PMID: 12643767 DOI: 10.1080/07391102.2003.10506881] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Bowman-Birk inhibitors (BBIs) are a well-studied family of canonical inhibitor proteins of serine proteinases. In nature, the active region of BBIs possesses a highly conserved Thr at the P2 position. The importance of this residue has been reemphasized by synthetic BBI reactive site loop proteinomimetics. In particular, this residue was exclusively identified for active chymotrypsin inhibitors selected from a BBI template-assisted combinatorial peptide library. A further kinetic analysis of 26 P2 variant peptides revealed that Thr provides both optimal binding affinity and optimal resistance against enzymatic turnover by chymotrypsin. Herein, we report the (1)H-NMR spectroscopic study of a 5-membered sub-set of these reactive site loop peptides representing a stepwise elimination of the Thr side-chain functionalities and inversion of its side-chain chirality. The P2 Thr variant adopts a three-dimensional structure that closely mimics the one of the corresponding region of the complete protein. This validates the use of this template for the investigation of structure-function relationships. While the overall backbone geometry is similar in all studied variants, conformational changes induced by the modification of the P2 side chain have now been identified and provide a rational explanation of the kinetically observed functional differences. Eliminating the gamma-methyl group has little structural effect, whereas the elimination of the gamma-oxygen atom or the inversion of the side-chain chirality results in characteristic changes to the intramolecular hydrogen bond network. We conclude that the transannular hydrogen bond between the P2 Thr side-chain hydroxyl and the P5' backbone amide is an important conformational constraint and directs the hydrophobic contact of the P2 Thr side chain with the enzyme surface in a functionally optimal geometry, both in the proteinomimetic and the native protein. In at least four canonical inhibitor protein families similar structural arrangements for a conserved P2 Thr have been observed, which suggests an analogous functional role. Substitutions at P2 of the proteinomimetic also affect the conformational balance between cis and trans isomers at a distant Pro-Pro motif (P3'-P4'). Presented with a mixture of cis/trans isomers chymotrypsin appears to interact preferably with the conformer that retains the cis-P3' Pro-trans-P4' Pro geometry found in the parent BBI protein.
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Affiliation(s)
- Arnd B E Brauer
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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Topf M, Várnai P, Richards WG. Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: insights into the active site hydrogen-bonding network. J Am Chem Soc 2002; 124:14780-8. [PMID: 12465991 DOI: 10.1021/ja026219q] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio QM/MM dynamics simulation is employed to examine the stability of the tetrahedral intermediate during the deacylation step in elastase-catalyzed hydrolysis of a simple peptide. An extended quantum region includes the catalytic triad, the tetrahedral structure, and the oxyanion hole. The calculations indicate that the tetrahedral intermediate of serine proteases is a stable species on the picosecond time scale. On the basis of geometrical and dynamical properties, and in agreement with many experimental and theoretical studies, it is suggested that the crucial hydrogen bonds involved in stabilizing this intermediate are between Asp-102 and His-57 and between the charged oxygen of the intermediate and the backbone N-H group of Gly-193 in the oxyanion hole. The mobility of the imidazolium ring between O(w) and O(gamma), two of the oxygens of the tetrahedral structure, shows how the intermediate could proceed toward the product state without a "ring-flip mechanism", proposed earlier on the basis of NMR data. In addition to the proposed C(epsilon)(1)-H.O hydrogen bond between the imidazolium ring and the backbone carbonyl of Ser-214, we observe an alternative C(epsilon)(1)-H.O hydrogen bond with the backbone carbonyl of Thr-213, that can stabilize the intermediate during the imidazolium movement. Proton hopping occurs between Asp-102 and His-57 during the simulation. The proton is, however, largely localized on the nitrogen, and hence it does not participate in a low-barrier hydrogen bond. The study also suggests factors that may be implicated in product release: breaking the hydrogen bond of the charged oxygen with the backbone of Ser-195 in the oxyanion hole and a loop opening between residues 216-225 that enables the breaking of a hydrogen bond in subsite S(3).
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Affiliation(s)
- Maya Topf
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QZ, United Kingdom.
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