1
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Dutta P, Sengupta N. Efficient Interrogation of the Kinetic Barriers Demarcating Catalytic States of a Tyrosine Kinase with Optimal Physical Descriptors and Mixture Models. Chemphyschem 2023; 24:e202200595. [PMID: 36394126 DOI: 10.1002/cphc.202200595] [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: 08/10/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Computer simulations are increasingly used to access thermo-kinetic information underlying structural transformation of protein kinases. Such information are necessary to probe their roles in disease progression and interactions with drug targets. However, the investigations are frequently challenged by forbiddingly high computational expense, and by the lack of standard protocols for the design of low dimensional physical descriptors that encode system features important for transitions. Here, we consider the demarcating characteristics of the different states of Abelson tyrosine kinase associated with distinct catalytic activity to construct a set of physically meaningful, orthogonal collective variables that preserve the slow modes of the system. Independent sampling of each metastable state is followed by the estimation of global partition function along the appropriate physical descriptors using the modified Expectation Maximized Molecular Dynamics method. The resultant free energy barriers are in excellent agreement with experimentally known rate-limiting dynamics and activation energy computed with conventional enhanced sampling methods. We discuss possible directions for further development and applications.
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Affiliation(s)
- Pallab Dutta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, India
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2
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Freire TS, Caracelli I, Zukerman-Schpector J, Friedman R. Resistance to a tyrosine kinase inhibitor mediated by changes to the conformation space of the kinase. Phys Chem Chem Phys 2023; 25:6175-6183. [PMID: 36752538 DOI: 10.1039/d2cp05549j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gilteritinib is a highly selective and effective inhibitor of the FLT3/ITD mutated protein, and is used successfully in treating acute myeloid leukaemia (AML). Unfortunately, tumour cells gradually develop resistance to gilteritinib due to mutations in the molecular drug target. The atomistic details behind this observed resistance are not clear, since the protein structure of the complex is only available in the inactive state, while the drug binds better to the active state. To overcome this limitation, we used a computer-aided approach where we docked gilteritinib to the active site of FLT3/ITD and calculated the Gibbs free energy difference between the binding energies of the parental and mutant enzymes. These calculations agreed with experimental estimations for one mutation (F691L) but not the other (D698N). To further understand how these mutations operate, we used metadynamics simulations to study the conformational landscape of the activation process. Both mutants show a lower activation energy barrier which suggests that they are more likely to adopt an active state until inhibited, making the mutant enzymes more active. This suggests that a higher efficiency of tyrosine kinases contributes to resistance not only against type 2 but also against type 1 kinase inhibitors.
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Affiliation(s)
- Thales Souza Freire
- Department of Physics, Federal University of São Carlos, São Carlos-SP, Brazil
| | - Ignez Caracelli
- Department of Physics, Federal University of São Carlos, São Carlos-SP, Brazil
| | | | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden.
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3
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Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. J Chem Inf Model 2022; 62:914-926. [PMID: 35138093 PMCID: PMC8889585 DOI: 10.1021/acs.jcim.1c00840] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 11/28/2022]
Abstract
The flexibility of β hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In this study, we have used apo Plm-II and BACE-1 as model systems. In the apo form of the proteases, a conserved tyrosine residue in the flap region remains in a dynamic equilibrium between the normal and flipped states through rotation of the χ1 and χ2 angles. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles (χ1 and χ2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilized by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.
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Affiliation(s)
- Soumendranath Bhakat
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
- Department
of Biochemistry and Molecular Biophysics, Washington University, School of Medicine, St. Louis, Missouri 63110, United States
| | - Pär Söderhjelm
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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4
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Oruganti B, Friedman R. Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path. J Chem Theory Comput 2021; 17:7260-7270. [PMID: 34647743 PMCID: PMC8582261 DOI: 10.1021/acs.jctc.1c00505] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Well-tempered metadynamics
(wT-metaD) simulations using path collective
variables (CVs) have been successfully applied in recent years to
explore conformational transitions in protein kinases and other biomolecular
systems. While this methodology has the advantage of describing the
transitions with a limited number of predefined path CVs, it requires
as an input a reference path connecting the initial and target states
of the system. It is desirable to automate the path generation using
approaches that do not rely on the choice of geometric CVs to describe
the transition of interest. To this end, we developed an approach
that couples essential dynamics sampling with wT-metaD simulations.
We used this newly developed procedure to explore the activation mechanism
of Abl1 kinase and compute the associated free energy barriers. Through
these simulations, we identified a three-step mechanism for the activation
that involved two metastable intermediates that possessed a partially
open activation loop and differed primarily in the “in”
or “out” conformation of the aspartate residue of the
DFG motif. One of these states is similar to a conformation that was
detected in previous spectroscopic studies of Abl1 kinase, albeit
its mechanistic role in the activation was hitherto not well understood.
The present study establishes its intermediary role in the activation
and predicts a rate-determining free energy barrier of 13.8 kcal/mol
that is in good agreement with previous experimental and computational
estimates. Overall, our study demonstrates the usability of essential
dynamics sampling as a path CV in wT-metaD to conveniently study conformational
transitions and accurately calculate the associated barriers.
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Affiliation(s)
- Baswanth Oruganti
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnæus University, 391 82 Kalmar, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnæus University, 391 82 Kalmar, Sweden
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5
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Friedman R, Bjelic S. Simulations Studies of Protein Kinases that are Molecular Targets in Cancer. Isr J Chem 2020. [DOI: 10.1002/ijch.202000015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ran Friedman
- Computational Chemistry and Biochemistry GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
| | - Sinisa Bjelic
- Protein Engineering GroupLinnæus UniversityDepartment of Chemistry and Biomedical Sciences Kalmar Sweden
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6
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Todde G, Friedman R. Activation and Inactivation of the FLT3 Kinase: Pathway Intermediates and the Free Energy of Transition. J Phys Chem B 2019; 123:5385-5394. [PMID: 31244095 DOI: 10.1021/acs.jpcb.9b01567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aberrant expression of kinases is often associated with pathologies such as cancer and autoimmune diseases. Like other types of enzymes, kinases can adopt active and inactive states, where a shift toward more stable active state often leads to disease. Dozens of kinase inhibitors are, therefore, used as drugs. Most of these bind to either the inactive or active state. In this work, we study the transitions between these two states in FLT3, an important drug target in leukemias. Kinases are composed of two lobes (N- and C-terminal lobes) with the catalytic site in-between. Through projection of the largest motions obtained through molecular dynamics (MD) simulations, we show that each of the end-states (active or inactive) already possess the ability for transition as the two lobes rotate which initiates the transition. A targeted simulation approach known as essential dynamics sampling (EDS) was used to speed up the transition between the two protein states. Coupling the EDS to implicit-solvent MD was performed to estimate the free energy barriers of the transitions. The activation energies were found in good agreement with previous estimates obtained for other kinases. Finally, we identified FLT3 intermediates that assumed configurations that resemble that of the c-Src nonreceptor tyrosine kinase. The intermediates show better binding to the drug ponatinib than c-Src and the inactive state of FLT3. This suggests that targeting intermediate states can be used to explain the drug-binding patterns of kinases and for rational drug design.
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Affiliation(s)
- Guido Todde
- Department of Chemistry ad Biomedical Sciences, Faculty of Health and Life Sciences , Linnæus University , 391 82 Kalmar , Sweden.,Linnæus University Centre of Exellence "Biomaterials Chemistry" , 391 82 Kalmar , Sweden
| | - Ran Friedman
- Department of Chemistry ad Biomedical Sciences, Faculty of Health and Life Sciences , Linnæus University , 391 82 Kalmar , Sweden.,Linnæus University Centre of Exellence "Biomaterials Chemistry" , 391 82 Kalmar , Sweden
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7
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Bobrovs R, Jaudzems K, Jirgensons A. Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. J Med Chem 2019; 62:8931-8950. [DOI: 10.1021/acs.jmedchem.9b00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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8
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Friedman R. The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib. Proteins 2017; 85:2143-2152. [PMID: 28799176 DOI: 10.1002/prot.25368] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/31/2022]
Abstract
Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is a drug target for leukemias. Several potent inhibitors of FLT3 exist, and bind to the inactive form of the enzyme. Unfortunately, resistance due to mutations in the kinase domain of FLT3 limits the therapeutic effects of these inhibitors. As in many other cases, it is not straightforward to explain why certain mutations lead to drug resistance. Extensive fully atomistic molecular dynamics (MD) simulations of FLT3 were carried out with an inhibited form (FLT-quizartinib complex), a free (apo) form, and an active conformation. In all cases, both the wild type (wt) proteins and two resistant mutants (D835F and Y842H) were studied. Analysis of the simulations revealed that impairment of protein-drug interactions cannot explain the resistance mutations in question. Rather, it appears that the active state of the mutant forms is perturbed by the mutations. It is therefore likely that perturbation of deactivation of the protein (which is necessary for drug binding) is responsible for the reduced affinity of the drug to the mutants. Importantly, this study suggests that it is possible to explain the source of resistance by mutations in FLT3 by an analysis of unbiased MD simulations.
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Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39 182 Kalmar, Sweden.,Centre of Excellence "Biomaterials Chemistry", Linnaeus University, 39 182 Kalmar, Sweden
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9
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Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 2016; 88:159-77. [PMID: 26872937 DOI: 10.1111/cbdd.12745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
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Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Soumendranath Bhakat
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
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10
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Kumari JLJ, Sudandiradoss C. Exploring the structural constraints at cleavage site of mucin 1 isoform through molecular dynamics simulation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:309-23. [DOI: 10.1007/s00249-015-1023-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/13/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022]
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11
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Park J, Chen YP, Perry Z, Li JR, Zhou HC. Preparation of core-shell coordination molecular assemblies via the enrichment of structure-directing "codes" of bridging ligands and metathesis of metal units. J Am Chem Soc 2014; 136:16895-901. [PMID: 25384026 DOI: 10.1021/ja508822r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A series of molybdenum- and copper-based MOPs were synthesized through coordination-driven process of a bridging ligand (3,3'-PDBAD, L(1)) and dimetal paddlewheel clusters. Three conformers of the ligand exist with an ideal bridging angle between the two carboxylate groups of 0° (H2α-L(1)), 120° (H2β-L(1)), and of 90° (H2γ-L(1)), respectively. At ambient or lower temperature, H2L(1) and Mo2(OAc)4 or Cu2(OAc)4 were crystallized into a molecular square with γ-L(1) and Mo2/Cu2 units. With proper temperature elevation, not only the molecular square with γ-L(1) but also a lantern-shaped cage with α-L(1) formed simultaneously. Similar to how Watson-Crick pairs stabilize the helical structure of duplex DNA, the core-shell molecular assembly possesses favorable H-bonding interaction sites. This is dictated by the ligand conformation in the shell, coding for the formation and providing stabilization of the central lantern shaped core, which was not observed without this complementary interaction. On the basis of the crystallographic implications, a heterobimetallic cage was obtained through a postsynthetic metal ion metathesis, showing different reactivity of coordination bonds in the core and shell. As an innovative synthetic strategy, the site-selective metathesis broadens the structural diversity and properties of coordination assemblies.
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Affiliation(s)
- Jinhee Park
- Department of Chemistry and Chemical Engineering, College of Environmental and Energy Engineering, Beijing University of Technology , Beijing, 100124, P. R. China
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12
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Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1224-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Autore F, Pagano B, Fornili A, Rittinger K, Fraternali F. In silico phosphorylation of the autoinhibited form of p47(phox): insights into the mechanism of activation. Biophys J 2010; 99:3716-25. [PMID: 21112296 PMCID: PMC2998635 DOI: 10.1016/j.bpj.2010.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/26/2010] [Accepted: 09/07/2010] [Indexed: 11/19/2022] Open
Abstract
Activation of the multicomponent enzyme NADPH oxidase requires the interaction between the tandem SH3 domain of the cytosolic subunit p47(phox) and the cytoplasmic tail of membrane-bound p22(phox). In the resting state, p47(phox) exists in an autoinhibited conformation stabilized by intramolecular contacts between the SH3 domains and an adjacent polybasic region. Phosphorylation of three serine residues, Ser(303), Ser(304), and Ser(328) within this polybasic region has been shown to be sufficient for the disruption of the intramolecular interactions thereby inducing an active state of p47(phox). This active conformation is accessible to the cytoplasmic tail of p22(phox) and initiates the formation of the membrane-bound functional enzyme complex. Molecular dynamics simulations reveal insights in the mechanism of activation of the autoinhibited form of p47(phox) by in silico phosphorylation, of the three serine residues, Ser(303), Ser(304), and Ser(328). The simulations highlight the major collective coordinates generating the opening and the closing of the two SH3 domains and the residues that cause the unmasking of the p22(phox) binding site.
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Affiliation(s)
- Flavia Autore
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
| | - Bruno Pagano
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, Fisciano, Italy
| | - Arianna Fornili
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
| | - Katrin Rittinger
- Division of Molecular Structure, MRC-National Institute for Medical Research, London, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
- KCL Centre for Bioinformatics, School of Physical Sciences & Engineering, King's College, London, United Kingdom
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14
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Fornili A, Giabbai B, Garau G, Degano M. Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures. J Am Chem Soc 2010; 132:17570-7. [DOI: 10.1021/ja107640u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arianna Fornili
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Barbara Giabbai
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Gianpiero Garau
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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15
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Friedman R, Caflisch A. On the orientation of the catalytic dyad in aspartic proteases. Proteins 2010; 78:1575-82. [PMID: 20112416 DOI: 10.1002/prot.22674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The recent re-refinement of the X-ray structure of apo plasmepsin II from Plasmodium falciparum suggests that the two carboxylate groups in the catalytic dyad are noncoplanar, (Robbins et al., Acta Crystallogr D Biol Crystallogr 2009;65: 294-296) in remarkable contrast with the vast majority of structures of aspartic proteases. Here, evidence for the noncoplanarity of the catalytic aspartates is provided by analysis of multiple explicit water molecular dynamics (MD) simulations of plasmepsin II, human beta-secretase, and HIV-protease. In the MD runs of plasmepsin II, the angle between the planes of the two carboxylates of the catalytic dyad is almost always in the range 60 degrees -120 degrees , in agreement with the perpendicular orientation in the re-refined X-ray structure. The noncoplanar arrangement is prevalent also in the beta-secretase simulations, as well as in the runs with the inhibitor-bound proteases. Quantum-mechanics calculations provide further evidence that before catalysis the noncoplanar arrangement is favored energetically in eukaryotic aspartic proteases. Remarkably, the coplanar orientation of the catalytic dyad is observed in MD simulations of HIV-protease at 100 K but not at 300 K, which indicates that the noncoplanar arrangement is favored by conformational entropy. This finding suggests that the coplanar orientation in the crystal structures of apo aspartic proteases is promoted by the very low temperature used for data collection (usually around 100 K).
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Affiliation(s)
- Ran Friedman
- Department of Biochemistry, University of Zürich, Switzerland.
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16
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Luksch T, Blum A, Klee N, Diederich W, Sotriffer C, Klebe G. Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein. ChemMedChem 2010; 5:443-54. [DOI: 10.1002/cmdc.200900452] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Parr-Vasquez CL, Yada RY. Functional chimera of porcine pepsin prosegment and Plasmodium falciparum plasmepsin II. Protein Eng Des Sel 2009; 23:19-26. [DOI: 10.1093/protein/gzp066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Ekonomiuk D, Caflisch A. Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. Protein Sci 2009; 18:1003-11. [PMID: 19388022 DOI: 10.1002/pro.110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The flaviviral nonstructural 3 protease (NS3pro) is essential for virus replication and is therefore a pharmaceutically relevant target to fight Dengue and West Nile virus (WNV). NS3pro is a chymotrypsin-like serine protease which requires a polypeptide cofactor (NS2B) for activation. Recent X-ray crystallography studies have led to the suggestion that the substrate binds to the two-component NS2B-NS3pro enzyme by an induced-fit mechanism. Here, multiple explicit water molecular dynamics simulations of the WNV NS2B-NS3pro enzyme show that the active conformation of the NS2B cofactor (in which its beta-loop is part of the substrate binding site) is stable over a 50-ns time scale even in the absence of the inhibitor. The partial and reversible opening of the NSB2 beta-loop and its correlated motion with an adjacent NS3pro loop, both observed in the simulations started from the active conformation, are likely to facilitate substrate binding and product release. Moreover, in five of eight simulations without inhibitor (started from two X-ray structures both with improperly formed oxyanion hole) the Thr132-Gly133 peptide bond flips spontaneously thereby promoting the formation of the catalytically competent oxyanion hole, which then stays stable until the end of the runs. The simulation results provide evidence at atomic level of detail that the substrate binds to the NS2B-NS3pro enzyme by conformational selection, rather than induced-fit mechanism.
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Affiliation(s)
- Dariusz Ekonomiuk
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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19
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Friedman R, Caflisch A. Discovery of Plasmepsin Inhibitors by Fragment-Based Docking and Consensus Scoring. ChemMedChem 2009; 4:1317-26. [DOI: 10.1002/cmdc.200900078] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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