1
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da Silva PCC, Martinez L. Extended Conformational Selection in the Antigen-Antibody Interaction of the PfAMA1 Protein. J Phys Chem B 2024; 128:8400-8408. [PMID: 39172501 DOI: 10.1021/acs.jpcb.4c03734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Plasmodium falciparum apical membrane antigen 1 (PfAMA1) is a surface protein found in two stages of the malaria life cycle. This is a protein involved in a reorientation movement of the parasite so that cell invasion occurs in the so-called "moving junction", relevant when the membranes of the parasite and the host are in contact. The structure of a conformational epitope of domain III of PfAMA1 in complex with the monoclonal antibody Fab F8.12.19 is experimentally known. Here, we used molecular dynamics with enhanced sampling by Hamiltonian replica exchange molecular dynamics (HREMD) to understand the effect of intermolecular interactions, conformational variability, and intrinsically disordered regions on the mechanism of antigen-antibody interaction. Clustering methods and the analysis of conformational variability were used in order to understand the influence of the presence of the partner protein in the complex. The free-state epitope accesses a broader conformational pool, including disordered conformations not seen in the bound state. The simulations suggest an extended conformational selection mechanism in which the antibody stabilizes a conformational set of the epitope existing in the free state. The stabilization of the active conformation occurs mainly through hydrogen bonds: Tyr(H33)-Asp493, His(L94)-Val510, Ser(L93)-Glu511, Tyr(H56)-Asp485, and Tyr(H35)-Asp493. The antibody has a structure with few flexible regions, and only the complementarity determining region (CDR) H3 shows greater plasticity in the presence of the epitope.
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Affiliation(s)
- Pamella Cristiny Carneiro da Silva
- Institute of Chemistry and Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
| | - Leandro Martinez
- Institute of Chemistry and Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
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2
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Pagán OR. The complexities of ligand/receptor interactions: Exploring the role of molecular vibrations and quantum tunnelling. Bioessays 2024; 46:e2300195. [PMID: 38459808 DOI: 10.1002/bies.202300195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/19/2024] [Accepted: 02/19/2024] [Indexed: 03/10/2024]
Abstract
Molecular vibrations and quantum tunneling may link ligand binding to the function of pharmacological receptors. The well-established lock-and-key model explains a ligand's binding and recognition by a receptor; however, a general mechanism by which receptors translate binding into activation, inactivation, or modulation remains elusive. The Vibration Theory of Olfaction was proposed in the 1930s to explain this subset of receptor-mediated phenomena by correlating odorant molecular vibrations to smell, but a mechanism was lacking. In the 1990s, inelastic electron tunneling was proposed as a plausible mechanism for translating molecular vibration to odorant physiology. More recently, studies of ligands' vibrational spectra and the use of deuterated ligand analogs have provided helpful information to study this admittedly controversial hypothesis in metabotropic receptors other than olfactory receptors. In the present work, based in part on published experiments from our laboratory using planarians as an experimental organism, I will present a rationale and possible experimental approach for extending this idea to ligand-gated ion channels.
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Affiliation(s)
- Oné R Pagán
- Department of Biology, West Chester University, West Chester, Pennsylvania, USA
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3
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Zhang Z, Cai Y, Zheng N, Deng Y, Gao L, Wang Q, Xia X. Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping. Biotechnol Adv 2024; 72:108346. [PMID: 38518963 DOI: 10.1016/j.biotechadv.2024.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yongchao Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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4
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Di Cera E. A simple method to resolve rate constants when the binding mechanism obeys induced fit or conformational selection. J Biol Chem 2024; 300:107131. [PMID: 38432634 PMCID: PMC10979105 DOI: 10.1016/j.jbc.2024.107131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/10/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
Many interactions involving a ligand and its molecular target are studied by rapid kinetics using a stopped-flow apparatus. Information obtained from these studies is often limited to a single, saturable relaxation that is insufficient to resolve all independent rate constants even for a two-step mechanism of binding obeying induced fit (IF) or conformational selection (CS). We introduce a simple method of general applicability where this limitation is overcome. The method accurately reproduces the rate constants for ligand binding to the serine protease thrombin determined independently from the analysis of multiple relaxations. Application to the inactive zymogen precursor of thrombin, prethrombin-2, resolves all rate constants for a binding mechanism of IF or CS from a single, saturable relaxation. Comparison with thrombin shows that the prethrombin-2 to thrombin conversion enhances ligand binding to the active site not by improving accessibility through the value of kon but by reducing the rate of dissociation koff. The conclusion holds regardless of whether binding is interpreted in terms of IF or CS and has general relevance for the mechanism of zymogen activation of serine proteases. The method also provides a simple test of the validity of IF and CS and indicates when more complex mechanisms of binding should be considered.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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5
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Wu D, Prem A, Xiao J, Salsbury FR. Thrombin - A Molecular Dynamics Perspective. Mini Rev Med Chem 2024; 24:1112-1124. [PMID: 37605420 DOI: 10.2174/1389557523666230821102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Thrombin is a crucial enzyme involved in blood coagulation, essential for maintaining circulatory system integrity and preventing excessive bleeding. However, thrombin is also implicated in pathological conditions such as thrombosis and cancer. Despite the application of various experimental techniques, including X-ray crystallography, NMR spectroscopy, and HDXMS, none of these methods can precisely detect thrombin's dynamics and conformational ensembles at high spatial and temporal resolution. Fortunately, molecular dynamics (MD) simulation, a computational technique that allows the investigation of molecular functions and dynamics in atomic detail, can be used to explore thrombin behavior. This review summarizes recent MD simulation studies on thrombin and its interactions with other biomolecules. Specifically, the 17 studies discussed here provide insights into thrombin's switch between 'slow' and 'fast' forms, active and inactive forms, the role of Na+ binding, the effects of light chain mutation, and thrombin's interactions with other biomolecules. The findings of these studies have significant implications for developing new therapies for thrombosis and cancer. By understanding thrombin's complex behavior, researchers can design more effective drugs and treatments that target thrombin.
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Affiliation(s)
- Dizhou Wu
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Athul Prem
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
- Freenome, South San Francisco, CA, 94080, USA
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
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6
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Sweeney DT, Zárate-Pérez F, Stokowa-Sołtys K, Hackett JC. Induced Fit Describes Ligand Binding to Membrane-Associated Cytochrome P450 3A4. Mol Pharmacol 2023; 104:154-163. [PMID: 37536953 PMCID: PMC10506697 DOI: 10.1124/molpharm.123.000698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Cytochrome P450 3A4 (CYP3A4) is the dominant P450 involved in human xenobiotic metabolism. Competition for CYP3A4 therefore underlies several adverse drug-drug interactions. Despite its clinical significance, the mechanisms CYP3A4 uses to bind diverse ligands remain poorly understood. Highly monodisperse CYP3A4 embedded in anionic lipoprotein nanodiscs containing an equal mixture of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) were used to determine which of the limiting kinetic schemes that include protein conformational change, conformational selection (CS) or induced fit (IF), best described the binding of four known irreversible inhibitors. Azamulin, retapamulin, pleuromutilin, and mibrefadil binding to CYP3A4 nanodiscs conformed to a single-site binding model. Exponential fits of stopped-flow UV-visible absorption spectroscopy data supported multiple-step binding mechanisms. Trends in the rates of relaxation to equilibrium with increasing ligand concentrations were ambiguous as to whether IF or CS was involved; however, global fitting and consideration of the rate constants favored an IF mechanism. In the case of mibrefadil, a transient complex was observed in the stopped-flow UV-visible experiment, definitively assigning the presence of IF in ligand binding. While these studies only consider a small region of CYP3A4's vast ligand space, they provide kinetic evidence that CYP3A4 can use an IF mechanism. SIGNIFICANCE STATEMENT: CYP3A4 is capable of oxidizing numerous xenobiotics, including many drugs. Such promiscuity could not be achieved without conformational changes to accommodate diverse substrates. It is unknown whether conformational heterogeneity is present before (conformational selection) or after (induced fit) ligand binding. Stopped-flow measurements of suicide inhibitors binding to nanodisc-embedded CYP3A4 combined with sophisticated numerical analyses support that induced fit better describes ligand binding to this important enzyme.
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Affiliation(s)
- David Tyler Sweeney
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - Francisco Zárate-Pérez
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - Kamila Stokowa-Sołtys
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
| | - John C Hackett
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida (J.C.H., K.S.S., F.Z.P.); Department of Physiology and Biophysics and The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia (D.T.S.); and Department of Biological and Medicinal Chemistry, Faculty of Chemistry, University of Wroclaw, Wroclaw, Poland (K.S.S.)
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7
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Redhair M, Nath A, Hackett JC, Atkins WM. Low molecular weight ligands bind to CYP3A4 via a branched induced fit mechanism: Implications for O 2 binding. Arch Biochem Biophys 2023; 739:109582. [PMID: 36948348 PMCID: PMC10103683 DOI: 10.1016/j.abb.2023.109582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/03/2023] [Accepted: 03/19/2023] [Indexed: 03/24/2023]
Affiliation(s)
- Michelle Redhair
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA, 98195-7610, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA, 98195-7610, USA
| | - John C Hackett
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th St., Miami, FL, 33199, USA
| | - William M Atkins
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA, 98195-7610, USA.
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8
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Sudhakar S, Barkau CL, Chilamkurthy R, Barber HM, Pater AA, Moran SD, Damha MJ, Pradeepkumar PI, Gagnon KT. Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly. J Biol Chem 2023; 299:104700. [PMID: 37059184 PMCID: PMC10200996 DOI: 10.1016/j.jbc.2023.104700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Ribonucleoproteins (RNPs) comprise one or more RNA and protein molecules that interact to form a stable complex, which commonly involves conformational changes in the more flexible RNA components. Here, we propose that Cas12a RNP assembly with its cognate CRISPR RNA (crRNA) guide instead proceeds primarily through Cas12a conformational changes during binding to more stable, prefolded crRNA 5' pseudoknot handles. Phylogenetic reconstructions and sequence and structure alignments revealed that the Cas12a proteins are divergent in sequence and structure while the crRNA 5' repeat region, which folds into a pseudoknot and anchors binding to Cas12a, is highly conserved. Molecular dynamics simulations of three Cas12a proteins and their cognate guides revealed substantial flexibility for unbound apo-Cas12a. In contrast, crRNA 5' pseudoknots were predicted to be stable and independently folded. Limited trypsin hydrolysis, differential scanning fluorimetry, thermal denaturation, and CD analyses supported conformational changes of Cas12a during RNP assembly and an independently folded crRNA 5' pseudoknot. This RNP assembly mechanism may be rationalized by evolutionary pressure to conserve CRISPR loci repeat sequence, and therefore guide RNA structure, to maintain function across all phases of the CRISPR defense mechanism.
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Affiliation(s)
- Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Christopher L Barkau
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Halle M Barber
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA.
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9
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Vauquelin G, Maes D. Competition in drug binding and … the race to equilibrium. Fundam Clin Pharmacol 2023; 37:147-157. [PMID: 35981720 DOI: 10.1111/fcp.12824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023]
Abstract
Binding kinetics has become a popular topic in pharmacology due to its potential contribution to the selectivity and duration of drug action. Yet, the overall kinetic aspects of complex binding mechanisms are still merely described in terms of elaborate algebraic equations. Interestingly, it has been recommended some 10 years ago to examine such mechanisms in terms of binding fluxes instead of the conventional rate constants. Alike the velocity of product formation in enzymology, those fluxes refer to the velocity by which one target species converts into another one. Novel binding flux-based approaches are utilized to get a better visual insight into the "competition" between two drugs/ligands for a single target as well as between induced fit- and conformational selection pathways for a single ligand within a thermodynamic cycle. The present data were obtained by differential equation-based simulations. Early on, the ligand-binding steps "race" to equilibrium (i.e., when their forward and reverse fluxes are equal) at their individual pace. The overall/global equilibrium is only reached later on. For the competition association assays, this parting might produce a transient "overshoot" of one of the bound target species. A similar overshoot may also show up within a thermodynamic cycle and, at first glance, suggest that the induced fit pathway dominates. Yet, present findings show that under certain circumstances, it could rather be the other way round. Novel binding flux-based approaches offer visually attractive insights into crucial aspects of "complex" binding mechanisms under non-equilibrium conditions.
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Affiliation(s)
- Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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10
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Biological Calorimetry: Old Friend, New Insights. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key aspects of biological calorimetry. Several biological systems will be described in which calorimetry was instrumental for modeling the behavior of the protein and obtaining further biological insight.
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11
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Guengerich FP. Roles of cytochrome P450 enzymes in pharmacology and toxicology: Past, present, and future. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:1-47. [PMID: 35953152 PMCID: PMC9869358 DOI: 10.1016/bs.apha.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of the cytochrome P450 (P450) field has been remarkable in the areas of pharmacology and toxicology, particularly in drug development. Today it is possible to use the knowledge base and relatively straightforward assays to make intelligent predictions about drug disposition prior to human dosing. Much is known about the structures, regulation, chemistry of catalysis, and the substrate and inhibitor specificity of human P450s. Many aspects of drug-drug interactions and side effects can be understood in terms of P450s. This knowledge has also been useful in pharmacy practice, as well as in the pharmaceutical industry and medical practice. However, there are still basic and practical questions to address regarding P450s and their roles in pharmacology and toxicology. Another aspect is the discovery of drugs that inhibit P450 to treat diseases.
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12
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Pelc LA, Koester SK, Kukla CR, Chen Z, Di Cera E. The active site region plays a critical role in Na + binding to thrombin. J Biol Chem 2022; 298:101458. [PMID: 34861239 PMCID: PMC8695361 DOI: 10.1016/j.jbc.2021.101458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 Å away from the catalytic residue S195, buried within the 180 and 220 loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+-binding site is in equilibrium between open (N) and closed (N∗) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N∗→N transition is strongly correlated with the analogous E∗→E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180 and 220 loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Cassandra R Kukla
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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13
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Redhair M, Atkins WM. Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection. Arch Biochem Biophys 2021; 714:109064. [PMID: 34715072 DOI: 10.1016/j.abb.2021.109064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
Ligand-dependent changes in protein conformation are foundational to biology. Historical mechanistic models for substrate-specific proteins are induced fit (IF) and conformational selection (CS), which invoke a change in protein conformation after ligand binds or before ligand binds, respectively. These mechanisms have important, but rarely discussed, functional relevance because IF vs. CS can differentially affect a protein's substrate specificity or promiscuity, and its regulatory properties. The modern view of proteins as conformational ensembles in both ligand free and bound states, together with the realization that most proteins exhibit some substrate promiscuity, demands a deeper interpretation of the historical models and provides an opportunity to improve mechanistic analyses. Here we describe alternative analytical strategies for distinguishing the historical models, including the more complex expanded versions of IF and CS. Functional implications of the different models are described. We provide an alternative perspective based on protein ensembles interacting with ligand ensembles that clarifies how a single protein can 'apparently' exploit different mechanisms for different ligands. Mechanistic information about protein ensembles can be optimized when they are probed with multiple ligands.
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Affiliation(s)
- Michelle Redhair
- Department of Medicinal Chemistry, Box 375610, University of Washington, Seattle, WA, 98177, USA
| | - William M Atkins
- Department of Medicinal Chemistry, Box 375610, University of Washington, Seattle, WA, 98177, USA.
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14
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Vauquelin G, Maes D. Induced fit versus conformational selection: From rate constants to fluxes… and back to rate constants. Pharmacol Res Perspect 2021; 9:e00847. [PMID: 34459109 PMCID: PMC8404059 DOI: 10.1002/prp2.847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/07/2021] [Indexed: 12/30/2022] Open
Abstract
Induced fit- (IF) and conformational selection (CS) binding mechanisms have long been regarded to be mutually exclusive. Yet, they are now increasingly considered to produce the final ligand-target complex alongside within a thermodynamic cycle. This viewpoint benefited from the introduction of binding fluxes as a tool for analyzing the overall behavior of such cycle. This study aims to provide more vivid and applicable insights into this emerging field. In this respect, combining differential equation- based simulations and hitherto little explored alternative modes of calculation provide concordant information about the intricate workings of such cycle. In line with previous reports, we observe that the relative contribution of IF increases with the ligand concentration at equilibrium. Yet the baseline contribution may vary from one case to another and simulations as well as calculations show that this parameter is essentially regulated by the dissociation rate of both pathways. Closer attention should be paid to how the contributions of IF and CS compare at physiologically relevant drug/ligand concentrations. To this end, a simple equation discloses how changing a limited set of "microscopic" rate constants can extend the concentration range at which CS contributes most effectively. Finally, it could also be beneficial to extend the utilization of flux- based approaches to more physiologically relevant time scales and alternative binding models.
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Affiliation(s)
- Georges Vauquelin
- Department Molecular and Biochemical PharmacologyVrije Universiteit BrusselBrusselsBelgium
| | - Dominique Maes
- Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
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15
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Extracellular loops of the serotonin transporter act as a selectivity filter for drug binding. J Biol Chem 2021; 297:100863. [PMID: 34118233 PMCID: PMC8253976 DOI: 10.1016/j.jbc.2021.100863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022] Open
Abstract
The serotonin transporter (SERT) shapes serotonergic neurotransmission by retrieving its eponymous substrate from the synaptic cleft. Ligands that discriminate between SERT and its close relative, the dopamine transporter DAT, differ in their association rate constant rather than their dissociation rate. The structural basis for this phenomenon is not known. Here we examined the hypothesis that the extracellular loops 2 (EL2) and 4 (EL4) limit access to the ligand-binding site of SERT. We employed an antibody directed against EL4 (residues 388–400) and the antibody fragments 8B6 scFv (directed against EL2 and EL4) and 15B8 Fab (directed against EL2) and analyzed their effects on the transport cycle of and inhibitor binding to SERT. Electrophysiological recordings showed that the EL4 antibody and 8B6 scFv impeded the initial substrate-induced transition from the outward to the inward-facing conformation but not the forward cycling mode of SERT. In contrast, binding of radiolabeled inhibitors to SERT was enhanced by either EL4- or EL2-directed antibodies. We confirmed this observation by determining the association and dissociation rate of the DAT-selective inhibitor methylphenidate via electrophysiological recordings; occupancy of EL2 with 15B8 Fab enhanced the affinity of SERT for methylphenidate by accelerating its binding. Based on these observations, we conclude that (i) EL4 undergoes a major movement during the transition from the outward to the inward-facing state, and (ii) EL2 and EL4 limit access of inhibitors to the binding of SERT, thus acting as a selectivity filter. This insight has repercussions for drug development.
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16
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Jankovic B, Ruf J, Zanobini C, Bozovic O, Buhrke D, Hamm P. Sequence of Events during Peptide Unbinding from RNase S: A Complete Experimental Description. J Phys Chem Lett 2021; 12:5201-5207. [PMID: 34038133 DOI: 10.1021/acs.jpclett.1c01155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phototriggered unbinding of the intrinsically disordered S-peptide from the RNase S complex is studied with the help of transient IR spectroscopy, covering a wide range of time scales from 100 ps to 10 ms. To that end, an azobenzene moiety has been linked to the S-peptide in a way that its helicity is disrupted by light, thereby initiating its complete unbinding. The full sequence of events is observed, starting from unfolding of the helical structure of the S-peptide on a 20 ns time scale while still being in the binding pocket of the S-protein, S-peptide unbinding after 300 μs, and the structural response of the S-protein after 3 ms. With regard to the S-peptide dynamics, the binding mechanism can be classified as an induced fit, while the structural response of the S-protein is better described as conformational selection.
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Affiliation(s)
- Brankica Jankovic
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Claudio Zanobini
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - David Buhrke
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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17
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Alleva C, Machtens JP, Kortzak D, Weyand I, Fahlke C. Molecular Basis of Coupled Transport and Anion Conduction in Excitatory Amino Acid Transporters. Neurochem Res 2021; 47:9-22. [PMID: 33587237 PMCID: PMC8763778 DOI: 10.1007/s11064-021-03252-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system. After its release from presynaptic nerve terminals, glutamate is quickly removed from the synaptic cleft by excitatory amino acid transporters (EAATs) 1–5, a subfamily of glutamate transporters. The five proteins utilize a complex transport stoichiometry that couples glutamate transport to the symport of three Na+ ions and one H+ in exchange with one K+ to accumulate glutamate against up to 106-fold concentration gradients. They are also anion-selective channels that open and close during transitions along the glutamate transport cycle. EAATs belong to a larger family of secondary-active transporters, the SLC1 family, which also includes purely Na+- or H+-coupled prokaryotic transporters and Na+-dependent neutral amino acid exchangers. In recent years, molecular cloning, heterologous expression, cellular electrophysiology, fluorescence spectroscopy, structural approaches, and molecular simulations have uncovered the molecular mechanisms of coupled transport, substrate selectivity, and anion conduction in EAAT glutamate transporters. Here we review recent findings on EAAT transport mechanisms, with special emphasis on the highly conserved hairpin 2 gate, which has emerged as the central processing unit in many of these functions.
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Affiliation(s)
- Claudia Alleva
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Jan-Philipp Machtens
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, Jülich, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
| | - Daniel Kortzak
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Ingo Weyand
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Christoph Fahlke
- Institute of Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum Jülich, Jülich, Germany.
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18
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Guengerich FP, Child SA, Barckhausen IR, Goldfarb MH. Kinetic Evidence for an Induced Fit Mechanism in the Binding of the Substrate Camphor by Cytochrome P450 cam. ACS Catal 2021; 11:639-649. [PMID: 34327042 PMCID: PMC8318206 DOI: 10.1021/acscatal.0c04455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial cytochrome P450 (P450) 101A1 (P450cam) has served as a prototype among the P450 enzymes and has high catalytic activity towards its cognate substrate, camphor. X-ray crystallography and NMR and IR spectroscopy have demonstrated the existence of multiple conformations of many P450s, including P450cam. Kinetic studies have indicated that substrate binding to several P450s is dominated by a conformational selection process, in which the substrate binds an individual conformer(s) of the unliganded enzyme. P450cam was found to differ in that binding of the substrate camphor is dominated by an induced fit mechanism, in which the enzyme binds camphor and then changes conformation, as evidenced by the equivalence of binding eigenvalues observed when varying both camphor and P450cam concentrations. The accessory protein putidaredoxin had no effect on substrate binding. Estimation of the rate of dissociation of the P450cam·camphor complex (15 s-1) and fitting of the data yield a minimal kinetic mechanism in which camphor binds (1.5 × 107 M-1 s-1) and the initial P450cam•camphor complex undergoes a reversible equilibrium (k forward 112 s-1, k reverse 28 s-1) to a final complex. This induced fit mechanism differs from those reported for several mammalian P450s and bacterial P450BM-3, indicative of the diversity of how P450s recognize multiple substrates. However, similar behavior was not observed with the alternate substrates (+)-α-pinene and 2-adamantanone, which probably utilize a conformational selection process.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Stella A Child
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Ian R Barckhausen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Margo H Goldfarb
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
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19
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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20
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Alleva C, Kovalev K, Astashkin R, Berndt MI, Baeken C, Balandin T, Gordeliy V, Fahlke C, Machtens JP. Na +-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters. SCIENCE ADVANCES 2020; 6:6/47/eaba9854. [PMID: 33208356 PMCID: PMC7673805 DOI: 10.1126/sciadv.aba9854] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 10/02/2020] [Indexed: 05/22/2023]
Abstract
Excitatory amino acid transporters (EAATs) harness [Na+], [K+], and [H+] gradients for fast and efficient glutamate removal from the synaptic cleft. Since each glutamate is cotransported with three Na+ ions, [Na+] gradients are the predominant driving force for glutamate uptake. We combined all-atom molecular dynamics simulations, fluorescence spectroscopy, and x-ray crystallography to study Na+:substrate coupling in the EAAT homolog GltPh A lipidic cubic phase x-ray crystal structure of wild-type, Na+-only bound GltPh at 2.5-Å resolution revealed the fully open, outward-facing state primed for subsequent substrate binding. Simulations and kinetic experiments established that only the binding of two Na+ ions to the Na1 and Na3 sites ensures complete HP2 gate opening via a conformational selection-like mechanism and enables high-affinity substrate binding via electrostatic attraction. The combination of Na+-stabilized gate opening and electrostatic coupling of aspartate to Na+ binding provides a constant Na+:substrate transport stoichiometry over a broad range of neurotransmitter concentrations.
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Affiliation(s)
- C Alleva
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
| | - K Kovalev
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - M I Berndt
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - V Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ch Fahlke
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - J-P Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, Jülich, Germany.
- Institute of Clinical Pharmacology, RWTH Aachen University, Aachen, Germany
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21
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins. Curr Res Struct Biol 2020; 2:180-190. [PMID: 34235478 PMCID: PMC8244415 DOI: 10.1016/j.crstbi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities. MBP operates by induced fit, HisJ by the conformational selection mechanism. Dual structure based models (dSBMs) encode two structures of a protein. MD simulations of dSBMs can identify the mechanism of conformational transitions. Locks, absent in HisJ, hold MBP open with ligand contacts required for closing. Binding mechanisms can be modified by altering such structural locks.
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Key Words
- BI, Balancing interface
- CS, conformational selection
- CTD, C-terminal domain
- Conformational selection
- Dual structure based models
- FEP, free energy profile
- HisJ, histidine binding protein
- IF, induced fit
- Induced fit
- MBP, maltose binding protein
- MD simulations
- MD, molecular dynamics
- NTD, N-terminal domain
- PBP, periplasmic binding protein
- Periplasmic binding proteins
- SH, spine helix
- Structural restraints
- WT, wild-type
- dSBM, dual structure-based model
- sSBM, single structure-based model
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22
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Ruben EA, Gandhi PS, Chen Z, Koester SK, DeKoster GT, Frieden C, Di Cera E. 19F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2. J Biol Chem 2020; 295:8227-8235. [PMID: 32358061 PMCID: PMC7294081 DOI: 10.1074/jbc.ra120.013419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Indexed: 11/06/2022] Open
Abstract
The conformational properties of trypsin-like proteases and their zymogen forms remain controversial because of a lack of sufficient information on their free forms. Specifically, it is unclear whether the free protease is zymogen-like and shifts to its mature form upon a ligand-induced fit or exists in multiple conformations in equilibrium from which the ligand selects the optimal fit via conformational selection. Here we report the results of 19F NMR measurements that reveal the conformational properties of a protease and its zymogen precursor in the free form. Using the trypsin-like, clotting protease thrombin as a relevant model system, we show that its conformation is quite different from that of its direct zymogen precursor prethrombin-2 and more similar to that of its fully active Na+-bound form. The results cast doubts on recent hypotheses that free thrombin is zymogen-like and transitions to protease-like forms upon ligand binding. Rather, they validate the scenario emerged from previous findings of X-ray crystallography and rapid kinetics supporting a pre-existing equilibrium between open (E) and closed (E*) forms of the active site. In this scenario, prethrombin-2 is more dynamic and exists predominantly in the E* form, whereas thrombin is more rigid and exists predominantly in the E form. Ligand binding to thrombin takes place exclusively in the E form without significant changes in the overall conformation. In summary, these results disclose the structural architecture of the free forms of thrombin and prethrombin-2, consistent with an E*-E equilibrium and providing no evidence that free thrombin is zymogen-like.
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Affiliation(s)
- Eliza A Ruben
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | | | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Sarah K Koester
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Gregory T DeKoster
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
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23
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Atkins WM. Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters. FEBS J 2020; 287:1306-1322. [PMID: 31663687 PMCID: PMC7138722 DOI: 10.1111/febs.15116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Detoxication, or 'drug-metabolizing', enzymes and drug transporters exhibit remarkable substrate promiscuity and catalytic promiscuity. In contrast to substrate-specific enzymes that participate in defined metabolic pathways, individual detoxication enzymes must cope with substrates of vast structural diversity, including previously unencountered environmental toxins. Presumably, evolution selects for a balance of 'adequate' kcat /KM values for a wide range of substrates, rather than optimizing kcat /KM for any individual substrate. However, the structural, energetic, and metabolic properties that achieve this balance, and hence optimize detoxication, are not well understood. Two features of detoxication enzymes that are frequently cited as contributions to promiscuity include the exploitation of highly reactive versatile cofactors, or cosubstrates, and a high degree of flexibility within the protein structure. This review examines these intuitive mechanisms in detail and clarifies the contributions of the classic ligand binding models 'induced fit' (IF) and 'conformational selection' (CS) to substrate promiscuity. The available literature data for drug metabolizing enzymes and transporters suggest that IF is exploited by these promiscuous detoxication enzymes, as it is with substrate-specific enzymes, but the detoxication enzymes uniquely exploit 'IFs' to retain a wide range of substrates at their active sites. In contrast, whereas CS provides no catalytic advantage to substrate-specific enzymes, promiscuous enzymes may uniquely exploit it to recruit a wide range of substrates. The combination of CS and IF, for recruitment and retention of substrates, can potentially optimize the promiscuity of drug metabolizing enzymes and drug transporters.
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Affiliation(s)
- William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWAUSA
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24
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Ivanov I, Verhamme IM, Sun MF, Mohammed B, Cheng Q, Matafonov A, Dickeson SK, Joseph K, Kaplan AP, Gailani D. Protease activity in single-chain prekallikrein. Blood 2020; 135:558-567. [PMID: 31800958 PMCID: PMC7033373 DOI: 10.1182/blood.2019002224] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
Prekallikrein (PK) is the precursor of the trypsin-like plasma protease kallikrein (PKa), which cleaves kininogens to release bradykinin and converts the protease precursor factor XII (FXII) to the enzyme FXIIa. PK and FXII undergo reciprocal conversion to their active forms (PKa and FXIIa) by a process that is accelerated by a variety of biological and artificial surfaces. The surface-mediated process is referred to as contact activation. Previously, we showed that FXII expresses a low level of proteolytic activity (independently of FXIIa) that may initiate reciprocal activation with PK. The current study was undertaken to determine whether PK expresses similar activity. Recombinant PK that cannot be converted to PKa was prepared by replacing Arg371 with alanine at the activation cleavage site (PK-R371A, or single-chain PK). Despite being constrained to the single-chain precursor form, PK-R371A cleaves high-molecular-weight kininogen (HK) to release bradykinin with a catalytic efficiency ∼1500-fold lower than that of kallikrein cleavage of HK. In the presence of a surface, PK-R371A converts FXII to FXIIa with a specific activity ∼4 orders of magnitude lower than for PKa cleavage of FXII. These results support the notion that activity intrinsic to PK and FXII can initiate reciprocal activation of FXII and PK in solution or on a surface. The findings are consistent with the hypothesis that the putative zymogens of many trypsin-like proteases are actually active proteases, explaining their capacity to undergo processes such as autoactivation and to initiate enzyme cascades.
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Affiliation(s)
- Ivan Ivanov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Mao-Fu Sun
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Bassem Mohammed
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Qiufang Cheng
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - Anton Matafonov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | - S Kent Dickeson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
| | | | - Allen P Kaplan
- Department of Medicine, Medical University of South Carolina, Charleston, SC
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
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25
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Role of the I16-D194 ionic interaction in the trypsin fold. Sci Rep 2019; 9:18035. [PMID: 31792294 PMCID: PMC6889508 DOI: 10.1038/s41598-019-54564-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Activity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
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26
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Goettig P, Brandstetter H, Magdolen V. Surface loops of trypsin-like serine proteases as determinants of function. Biochimie 2019; 166:52-76. [PMID: 31505212 PMCID: PMC7615277 DOI: 10.1016/j.biochi.2019.09.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Trypsin and chymotrypsin-like serine proteases from family S1 (clan PA) constitute the largest protease group in humans and more generally in vertebrates. The prototypes chymotrypsin, trypsin and elastase represent simple digestive proteases in the gut, where they cleave nearly any protein. Multidomain trypsin-like proteases are key players in the tightly controlled blood coagulation and complement systems, as well as related proteases that are secreted from diverse immune cells. Some serine proteases are expressed in nearly all tissues and fluids of the human body, such as the human kallikreins and kallikrein-related peptidases with specialization for often unique substrates and accurate timing of activity. HtrA and membrane-anchored serine proteases fulfill important physiological tasks with emerging roles in cancer. The high diversity of all family members, which share the tandem β-barrel architecture of the chymotrypsin-fold in the catalytic domain, is conferred by the large differences of eight surface loops, surrounding the active site. The length of these loops alters with insertions and deletions, resulting in remarkably different three-dimensional arrangements. In addition, metal binding sites for Na+, Ca2+ and Zn2+ serve as regulatory elements, as do N-glycosylation sites. Depending on the individual tasks of the protease, the surface loops determine substrate specificity, control the turnover and allow regulation of activation, activity and degradation by other proteins, which are often serine proteases themselves. Most intriguingly, in some serine proteases, the surface loops interact as allosteric network, partially tuned by protein co-factors. Knowledge of these subtle and complicated molecular motions may allow nowadays for new and specific pharmaceutical or medical approaches.
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Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| | - Hans Brandstetter
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Viktor Magdolen
- Clinical Research Unit, Department of Obstetrics and Gynecology, School of Medicine, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany
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27
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Yang J, Gao M, Xiong J, Su Z, Huang Y. Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Sci 2019; 28:1952-1965. [PMID: 31441158 PMCID: PMC6798136 DOI: 10.1002/pro.3718] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
The sequence-structure-function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well-defined three-dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.
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Affiliation(s)
- Jing Yang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Meng Gao
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Junwen Xiong
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Zhengding Su
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
| | - Yongqi Huang
- Department of Biological Engineering and Key Laboratory of Industrial Fermentation (Ministry of Education)Hubei University of TechnologyWuhanHubeiChina
- Institute of Biomedical and Pharmaceutical SciencesHubei University of TechnologyWuhanHubeiChina
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28
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Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep 2019; 9:12304. [PMID: 31444378 PMCID: PMC6707225 DOI: 10.1038/s41598-019-48839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 01/07/2023] Open
Abstract
A pre-existing, allosteric equilibrium between closed (E*) and open (E) conformations of the active site influences the level of activity in the trypsin fold and defines ligand binding according to the mechanism of conformational selection. Using the clotting protease thrombin as a model system, we investigate the molecular determinants of the E*-E equilibrium through rapid kinetics and X-ray structural biology. The equilibrium is controlled by three residues positioned around the active site. W215 on the 215-217 segment defining the west wall of the active site controls the rate of transition from E to E* through hydrophobic interaction with F227. E192 on the opposite 190-193 segment defining the east wall of the active site controls the rate of transition from E* to E through electrostatic repulsion of E217. The side chain of E217 acts as a lever that moves the entire 215-217 segment in the E*-E equilibrium. Removal of this side chain converts binding to the active site to a simple lock-and-key mechanism and freezes the conformation in a state intermediate between E* and E. These findings reveal a simple framework to understand the molecular basis of a key allosteric property of the trypsin fold.
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29
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Guengerich FP, Wilkey CJ, Phan TTN. Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes. J Biol Chem 2019; 294:10928-10941. [PMID: 31147443 DOI: 10.1074/jbc.ra119.009305] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/29/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450) enzymes are major catalysts involved in the oxidations of most drugs, steroids, carcinogens, fat-soluble vitamins, and natural products. The binding of substrates to some of the 57 human P450s and other mammalian P450s is more complex than a two-state system and has been proposed to involve mechanisms such as multiple ligand occupancy, induced-fit, and conformational-selection. Here, we used kinetic analysis of binding with multiple concentrations of substrates and computational modeling of these data to discern possible binding modes of several human P450s. We observed that P450 2D6 binds its ligand rolapitant in a mechanism involving conformational-selection. P450 4A11 bound the substrate lauric acid via conformational-selection, as did P450 2C8 with palmitic acid. Binding of the steroid progesterone to P450 21A2 was also best described by a conformational-selection model. Hexyl isonicotinate binding to P450 2E1 could be described by either a conformational-selection or an induced-fit model. Simulation of the binding of the ligands midazolam, bromocriptine, testosterone, and ketoconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the concentration dependence of binding rates for varying both P450 3A4 and midazolam concentrations revealed discordance in the parameters, indicative of conformational-selection. Binding of the P450s 2C8, 2D6, 3A4, 4A11, and 21A2 was best described by conformational-selection, and P450 2E1 appeared to fit either mode. These findings highlight the complexity of human P450-substrate interactions and that conformational-selection is a dominant feature of many of these interactions.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
| | - Clayton J Wilkey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Thanh T N Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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30
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Mesrouze Y, Bokhovchuk F, Izaac A, Meyerhofer M, Zimmermann C, Fontana P, Schmelzle T, Erdmann D, Furet P, Kallen J, Chène P. Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface. Protein Sci 2019; 27:1810-1820. [PMID: 30058229 DOI: 10.1002/pro.3493] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023]
Abstract
Many interactions between proteins are mediated by intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) do not adopt a stable three-dimensional structure in their unbound form, but they become more structured upon binding to their partners. In this communication, we study how a bound IDR adapts to mutations, preventing the formation of hydrogen bonds at the binding interface that needs a precise positioning of the interacting residues to be formed. We use as a model the YAP:TEAD interface, where one YAP (IDP) and two TEAD residues form hydrogen bonds via their side chain. Our study shows that the conformational flexibility of bound YAP and the reorganization of water molecules at the interface help to reduce the energetic constraints created by the loss of H-bonds at the interface. The residual flexibility/dynamic of bound IDRs and water might, therefore, be a key for the adaptation of IDPs to different interface landscapes and to mutations occurring at binding interfaces.
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Affiliation(s)
- Yannick Mesrouze
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fedir Bokhovchuk
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Aude Izaac
- Chemical Biology & Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marco Meyerhofer
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Catherine Zimmermann
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Patrizia Fontana
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tobias Schmelzle
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Erdmann
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Pascal Furet
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Joerg Kallen
- Chemical Biology & Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Patrick Chène
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
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31
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Guengerich FP, Wilkey CJ, Glass SM, Reddish MJ. Conformational selection dominates binding of steroids to human cytochrome P450 17A1. J Biol Chem 2019; 294:10028-10041. [PMID: 31072872 DOI: 10.1074/jbc.ra119.008860] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 (P450, CYP) enzymes are the major catalysts involved in the oxidation of steroids as well as many other compounds. Their versatility has been explained in part by flexibility of the proteins and complexity of the binding mechanisms. However, whether these proteins bind their substrates via induced fit or conformational selection is not understood. P450 17A1 has a major role in steroidogenesis, catalyzing the two-step oxidations of progesterone and pregnenolone to androstenedione and dehydroepiandrosterone, respectively, via 17α-hydroxy (OH) intermediates. We examined the interaction of P450 17A1 with its steroid substrates by analyzing progress curves (UV-visible spectroscopy), revealing that the rates of binding of any of these substrates decreased with increasing substrate concentration, a hallmark of conformational selection. Further, when the concentration of 17α-OH pregnenolone was held constant and the P450 concentration increased, the binding rate increased, and such opposite patterns are also diagnostic of conformational selection. Kinetic simulation modeling was also more consistent with conformational selection than with an induced-fit mechanism. Cytochrome b 5 partially enhances P450 17A1 lyase activity by altering the P450 17A1 conformation but did not measurably alter the binding of 17α-OH pregnenolone or 17α-OH progesterone, as judged by the apparent Kd and binding kinetics. The P450 17A1 inhibitor abiraterone also bound to P450 17A1 in a multistep manner, and modeling indicated that the selective inhibition of the two P450 17A1 steps by the drug orteronel can be rationalized only by a multiple-conformation model. In conclusion, P450 17A1 binds its steroid substrates via conformational selection.
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Affiliation(s)
- F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Clayton J Wilkey
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Sarah M Glass
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Michael J Reddish
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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32
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Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J. Engineering enzyme access tunnels. Biotechnol Adv 2019; 37:107386. [PMID: 31026496 DOI: 10.1016/j.biotechadv.2019.04.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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33
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Welty R, Pabit SA, Katz AM, Calvey GD, Pollack L, Hall KB. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA (NEW YORK, N.Y.) 2018; 24:1828-1838. [PMID: 30254137 PMCID: PMC6239185 DOI: 10.1261/rna.068361.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 05/22/2023]
Abstract
Folding of an RNA from secondary to tertiary structure often depends on divalent ions for efficient electrostatic charge screening (nonspecific association) or binding (specific association). To measure how different divalent cations modify folding kinetics of the 60 nucleotide Ecoli rRNA GTPase center, we combined stopped-flow fluorescence in the presence of Mg2+, Ca2+, or Sr2+ together with time-resolved small angle X-ray scattering (SAXS) in the presence of Mg2+ to observe the folding process. Immediately upon addition of each divalent ion, the RNA undergoes a transition from an extended state with secondary structure to a more compact structure. Subsequently, specific divalent ions modulate populations of intermediates in conformational ensembles along the folding pathway with transition times longer than 10 msec. Rate constants for the five folding transitions act on timescales from submillisecond to tens of seconds. The sensitivity of RNA tertiary structure to divalent cation identity affects all but the fastest events in RNA folding, and allowed us to identify those states that prefer Mg2+ The GTPase center RNA appears to have optimized its folding trajectory to specifically utilize this most abundant intracellular divalent ion.
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Affiliation(s)
- Robb Welty
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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34
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Liu L, Stepanian L, Dubins DN, Chalikian TV. Binding of l-Argininamide to a DNA Aptamer: A Volumetric Study. J Phys Chem B 2018; 122:7647-7653. [PMID: 30011203 DOI: 10.1021/acs.jpcb.8b03912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use a combination of volumetric and spectroscopic techniques to characterize the binding of l-argininamide to its aptamer, the 24-base DNA hairpin 5'-d(GATCGAAACGTAGCGCCTTCGATC)-3'. The binding causes increases in volume, Δ V, and adiabatic compressibility, Δ KS, of 12 ± 7 cm3 mol-1 bar and (73 ± 8) × 10-4 cm3 mol-1 bar-1, respectively. These volumetric results combined with structural data reveal that the binding is accompanied by release of 73 ± 27 waters from the hydration shells of the interacting molecules to the bulk. We use the estimated change in hydration to estimate the hydration, Δ Shyd, and configurational, Δ Sconf, contributions to the binding entropy. The large and unfavorable change in configurational entropy, Δ Sconf, is nearly compensated by a favorable change in the hydration contribution, Δ Shyd.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Lora Stepanian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - David N Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
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35
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Gülbakan B, Barylyuk K, Schneider P, Pillong M, Schneider G, Zenobi R. Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. J Am Chem Soc 2018; 140:7486-7497. [DOI: 10.1021/jacs.7b13044] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Basri Gülbakan
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
- Hacettepe University Institute of Child Health, Ihsan Dogramaci Children’s Hospital, Sıhhiye Square, 06100 Ankara, Turkey
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Max Pillong
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
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36
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Chakraborty P, Acquasaliente L, Pelc LA, Di Cera E. Interplay between conformational selection and zymogen activation. Sci Rep 2018; 8:4080. [PMID: 29511224 PMCID: PMC5840343 DOI: 10.1038/s41598-018-21728-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/09/2018] [Indexed: 11/09/2022] Open
Abstract
Trypsin-like proteases are synthesized as zymogens and activated through a mechanism that folds the active site for efficient binding and catalysis. Ligand binding to the active site is therefore a valuable source of information on the changes that accompany zymogen activation. Using the physiologically relevant transition of the clotting zymogen prothrombin to the mature protease thrombin, we show that the mechanism of ligand recognition follows selection within a pre-existing ensemble of conformations with the active site accessible (E) or inaccessible (E*) to binding. Prothrombin exists mainly in the E* conformational ensemble and conversion to thrombin produces two dominant changes: a progressive shift toward the E conformational ensemble triggered by removal of the auxiliary domains upon cleavage at R271 and a drastic drop of the rate of ligand dissociation from the active site triggered by cleavage at R320. Together, these effects produce a significant (700-fold) increase in binding affinity. Limited proteolysis reveals how the E*-E equilibrium shifts during prothrombin activation and influences exposure of the sites of cleavage at R271 and R320. These new findings on the molecular underpinnings of prothrombin activation are relevant to other zymogens with modular assembly involved in blood coagulation, complement and fibrinolysis.
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Affiliation(s)
- Pradipta Chakraborty
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Laura Acquasaliente
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
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37
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Li MJ, Guttman M, Atkins WM. Conformational dynamics of P-glycoprotein in lipid nanodiscs and detergent micelles reveal complex motions on a wide time scale. J Biol Chem 2018; 293:6297-6307. [PMID: 29511086 DOI: 10.1074/jbc.ra118.002190] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Indexed: 11/06/2022] Open
Abstract
P-glycoprotein (P-gp) is a highly substrate-promiscuous efflux transporter that plays a critical role in drug disposition. P-gp utilizes ATP hydrolysis by nucleotide-binding domains (NBDs) to drive transitions between inward-facing (IF) conformations that bind drugs and outward-facing (OF) conformations that release them to the extracellular solution. However, the details of the protein dynamics within either macroscopic IF or OF conformation remain uncharacterized, and the functional role of local dynamics has not been determined. In this work we measured the local dynamics of the IF state of P-gp in lipid nanodiscs and in detergent solution by hydrogen-deuterium (H/D) exchange MS. We observed "EX1 exchange kinetics," or bimodal kinetics, for several peptides distributed in both NBDs, particularly for P-gp in the lipid nanodiscs. Remarkably, the EX1 kinetics occurred on several time scales, ranging from seconds to hours, suggesting highly complex, and correlated, motions. The results indicate at least three distinct conformational states in the ligand-free P-gp and suggest a rough conformational landscape. Addition of excess ATP and vanadate, to favor the OF conformations, caused a generalized, but modest, decrease in H/D exchange throughout the NBDs and slowed the EX1 kinetic transitions of several peptides. The functional implications of the results are consistent with the possibility that conformational selection provides a source of substrate promiscuity.
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Affiliation(s)
- Mavis Jiarong Li
- From the Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
| | - Miklos Guttman
- From the Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
| | - William M Atkins
- From the Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610
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38
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"Multiple partial recognitions in dynamic equilibrium" in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands. Biophys Rev 2017; 10:421-433. [PMID: 29243092 DOI: 10.1007/s12551-017-0365-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/19/2017] [Indexed: 12/12/2022] Open
Abstract
Promiscuous recognition of ligands by proteins is as important as strict recognition in numerous biological processes. In living cells, many short, linear amino acid motifs function as targeting signals in proteins to specify the final destination of the protein transport. In general, the target signal is defined by a consensus sequence containing wild-characters, and hence represented by diverse amino acid sequences. The classical lock-and-key or induced-fit/conformational selection mechanism may not cover all aspects of the promiscuous recognition. On the basis of our crystallographic and NMR studies on the mitochondrial Tom20 protein-presequence interaction, we proposed a new hypothetical mechanism based on "a rapid equilibrium of multiple states with partial recognitions". This dynamic, multiple recognition mode enables the Tom20 receptor to recognize diverse mitochondrial presequences with nearly equal affinities. The plant Tom20 is evolutionally unrelated to the animal Tom20 in our study, but is a functional homolog of the animal/fungal Tom20. NMR studies by another research group revealed that the presequence binding by the plant Tom20 was not fully explained by simple interaction modes, suggesting the presence of a similar dynamic, multiple recognition mode. Circumstantial evidence also suggested that similar dynamic mechanisms may be applicable to other promiscuous recognitions of signal peptides by the SRP54/Ffh and SecA proteins.
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39
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Gleitsman KR, Sengupta RN, Herschlag D. Slow molecular recognition by RNA. RNA (NEW YORK, N.Y.) 2017; 23:1745-1753. [PMID: 28971853 PMCID: PMC5688996 DOI: 10.1261/rna.062026.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/26/2017] [Indexed: 05/28/2023]
Abstract
Molecular recognition is central to biological processes, function, and specificity. Proteins associate with ligands with a wide range of association rate constants, with maximal values matching the theoretical limit set by the rate of diffusional collision. As less is known about RNA association, we compiled association rate constants for all RNA/ligand complexes that we could find in the literature. Like proteins, RNAs exhibit a wide range of association rate constants. However, the fastest RNA association rates are considerably slower than those of the fastest protein associations and fall well below the diffusional limit. The apparently general observation of slow association with RNAs has implications for evolution and for modern-day biology. Our compilation highlights a quantitative molecular property that can contribute to biological understanding and underscores our need to develop a deeper physical understanding of molecular recognition events.
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Affiliation(s)
- Kristin R Gleitsman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Raghuvir N Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Chemical Engineering and Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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