1
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Mandal N, Surpeta B, Brezovsky J. Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J Chem Inf Model 2024. [PMID: 39143923 DOI: 10.1021/acs.jcim.4c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Tunnels are structural conduits in biomolecules responsible for transporting chemical compounds and solvent molecules from the active site. They have been shown to be present in a wide variety of enzymes across all functional and structural classes. However, the study of such pathways is experimentally challenging, because they are typically transient. Computational methods, such as molecular dynamics (MD) simulations, have been successfully proposed to explore tunnels. Conventional MD (cMD) provides structural details to characterize tunnels but suffers from sampling limitations to capture rare tunnel openings on longer time scales. Therefore, in this study, we explored the potential of Gaussian accelerated MD (GaMD) simulations to improve the exploration of complex tunnel networks in enzymes. We used the haloalkane dehalogenase LinB and its two variants with engineered transport pathways, which are not only well-known for their application potential but have also been extensively studied experimentally and computationally regarding their tunnel networks and their importance in multistep catalytic reactions. Our study demonstrates that GaMD efficiently improves tunnel sampling and allows the identification of all known tunnels for LinB and its two mutants. Furthermore, the improved sampling provided insight into a previously unknown transient side tunnel (ST). The extensive conformational landscape explored by GaMD simulations allowed us to investigate in detail the mechanism of ST opening. We determined variant-specific dynamic properties of ST opening, which were previously inaccessible due to limited sampling of cMD. Our comprehensive analysis supports multiple indicators of the functional relevance of the ST, emphasizing its potential significance beyond structural considerations. In conclusion, our research proves that the GaMD method can overcome the sampling limitations of cMD for the effective study of tunnels in enzymes, providing further means for identifying rare tunnels in enzymes with the potential for drug development, precision medicine, and rational protein engineering.
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Affiliation(s)
- Nishita Mandal
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Bartlomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, Poznan 61-614, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, Warsaw 02-109, Poland
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2
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Sohraby F, Nunes-Alves A. Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. J Chem Inf Model 2024; 64:4193-4203. [PMID: 38728115 PMCID: PMC11134402 DOI: 10.1021/acs.jcim.4c00187] [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: 02/02/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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3
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Croney K, McCarty J. Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. J Phys Chem B 2024; 128:3102-3112. [PMID: 38516924 PMCID: PMC11000218 DOI: 10.1021/acs.jpcb.3c07972] [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: 12/05/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The yeast cytosine deaminase (yCD) enzyme/5-fluorocytosine prodrug system is a promising candidate for targeted chemotherapeutics. After conversion of the prodrug into the toxic chemotherapeutic drug, 5-fluorouracil (5-FU), the slow product release from the enzyme limits the overall catalytic efficiency of the enzyme/prodrug system. Here, we present a computational study of the product release of the anticancer drug, 5-FU, from yCD using metadynamics. We present a comparison of the 5-FU drug to the natural enzyme product, uracil. We use volume-based metadynamics to compute the free energy landscape for product release and show a modest binding affinity for the product to the enzyme, consistent with experiments. Next, we use infrequent metadynamics to estimate the unbiased release rate from Kramers time-dependent rate theory and find a favorable comparison to experiment with a slower rate of product release for the 5-FU system. Our work demonstrates how adaptive sampling methods can be used to study the protein-ligand unbinding process for engineering enzyme/prodrug systems and gives insights into the molecular mechanism of product release for the yCD/5-FU system.
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Affiliation(s)
- Kayla
A. Croney
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
| | - James McCarty
- Department of Chemistry, Western
Washington University, Bellingham, Washington 98225, United States
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4
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Chen H, Guo Y, Ye S, Zhang J, Zhang H, Liu N, Zhou R, Hou T, Xia H, Kang Y, Duan M. On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J Chem Inf Model 2023; 63:5232-5243. [PMID: 37574904 DOI: 10.1021/acs.jcim.3c00641] [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: 08/15/2023]
Abstract
Fatty acids (FAs) are one of the essential energy sources for physiological processes, and they play a vital role in regulating immune and inflammatory responses, promoting cell differentiation and apoptosis, and inhibiting tumor growth. These functions are carried out by FA binding proteins (FABPs) that recognize and transport FAs. Although the crystal structure of the FA-FABPs complex has long been characterized, the mechanism behind FA binding and dissociation from FABP remains unclear. This study employed conventional MD simulations and enhanced sampling technologies to investigate the atomic-scale complexes of heart fatty acid binding proteins and stearic acid (SA). The results revealed two primary pathways for the binding or dissociation of the flexible long-chain ligand, with the orientation of the SA carboxyl head during dissociation determining the chosen path. Conformational changes in the portal region of FABP during the ligand binding/unbinding were found to be trivial, and the overturn of the ″cap″ or the unfolding of the α2 helix was not required. This study resolves the long-standing debate on the binding mechanism of SA with the long-flexible tail to FABP, which significantly improves the understanding of the transport mechanism of FABPs and the development of related therapeutic agents.
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Affiliation(s)
- Haiyi Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Yue Guo
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shengqing Ye
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Jintu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Haotian Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Na Liu
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongguang Xia
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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5
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Niklas B, Rydzewski J, Lapied B, Nowak W. Toward Overcoming Pyrethroid Resistance in Mosquito Control: The Role of Sodium Channel Blocker Insecticides. Int J Mol Sci 2023; 24:10334. [PMID: 37373481 DOI: 10.3390/ijms241210334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Diseases spread by mosquitoes lead to the death of 700,000 people each year. The main way to reduce transmission is vector control by biting prevention with chemicals. However, the most commonly used insecticides lose efficacy due to the growing resistance. Voltage-gated sodium channels (VGSCs), membrane proteins responsible for the depolarizing phase of an action potential, are targeted by a broad range of neurotoxins, including pyrethroids and sodium channel blocker insecticides (SCBIs). Reduced sensitivity of the target protein due to the point mutations threatened malaria control with pyrethroids. Although SCBIs-indoxacarb (a pre-insecticide bioactivated to DCJW in insects) and metaflumizone-are used in agriculture only, they emerge as promising candidates in mosquito control. Therefore, a thorough understanding of molecular mechanisms of SCBIs action is urgently needed to break the resistance and stop disease transmission. In this study, by performing an extensive combination of equilibrium and enhanced sampling molecular dynamics simulations (3.2 μs in total), we found the DIII-DIV fenestration to be the most probable entry route of DCJW to the central cavity of mosquito VGSC. Our study revealed that F1852 is crucial in limiting SCBI access to their binding site. Our results explain the role of the F1852T mutation found in resistant insects and the increased toxicity of DCJW compared to its bulkier parent compound, indoxacarb. We also delineated residues that contribute to both SCBIs and non-ester pyrethroid etofenprox binding and thus could be involved in the target site cross-resistance.
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Affiliation(s)
- Beata Niklas
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - Bruno Lapied
- University Angers, INRAE, SIFCIR, SFR QUASAV, F-49045 Angers, France
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
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6
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Rydzewski J. Selecting High-Dimensional Representations of Physical Systems by Reweighted Diffusion Maps. J Phys Chem Lett 2023; 14:2778-2783. [PMID: 36897996 PMCID: PMC10041639 DOI: 10.1021/acs.jpclett.3c00265] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Constructing reduced representations of high-dimensional systems is a fundamental problem in physical chemistry. Many unsupervised machine learning methods can automatically find such low-dimensional representations. However, an often overlooked problem is what high-dimensional representation should be used to describe systems before dimensionality reduction. Here, we address this issue using a recently developed method called the reweighted diffusion map [J. Chem. Theory Comput. 2022, 18, 7179-7192]. We show how high-dimensional representations can be quantitatively selected by exploring the spectral decomposition of Markov transition matrices built from data obtained from standard or enhanced sampling atomistic simulations. We demonstrate the performance of the method in several high-dimensional examples.
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7
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Mitusińska K, Bzówka M, Magdziarz T, Góra A. Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls. J Chem Inf Model 2022; 62:6803-6811. [PMID: 36374085 PMCID: PMC9795556 DOI: 10.1021/acs.jcim.2c00985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits and pitfalls. Results obtained for both crystal structures and molecular dynamics (MD) simulations were analyzed to investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential for the low-diameter tunnel description, and assessment of the tunnel functionality based only on their geometrical parameters is challenging. We showed that the small-molecule tracking approach can provide a detailed description of the system; however, it can also be the most computationally demanding.
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8
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Rydzewski J, Chen M, Ghosh TK, Valsson O. Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations. J Chem Theory Comput 2022; 18:7179-7192. [PMID: 36367826 DOI: 10.1021/acs.jctc.2c00873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of such enhanced sampling methods works by identifying a few slow degrees of freedom, termed collective variables (CVs), and enhancing the sampling along these CVs. Selecting CVs to analyze and drive the sampling is not trivial and often relies on chemical intuition. Despite routinely circumventing this issue using manifold learning to estimate CVs directly from standard simulations, such methods cannot provide mappings to a low-dimensional manifold from enhanced sampling simulations, as the geometry and density of the learned manifold are biased. Here, we address this crucial issue and provide a general reweighting framework based on anisotropic diffusion maps for manifold learning that takes into account that the learning data set is sampled from a biased probability distribution. We consider manifold learning methods based on constructing a Markov chain describing transition probabilities between high-dimensional samples. We show that our framework reverts the biasing effect, yielding CVs that correctly describe the equilibrium density. This advancement enables the construction of low-dimensional CVs using manifold learning directly from the data generated by enhanced sampling simulations. We call our framework reweighted manifold learning. We show that it can be used in many manifold learning techniques on data from both standard and enhanced sampling simulations.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Ming Chen
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tushar K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Omar Valsson
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
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9
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Vavra O, Damborsky J, Bednar D. Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies. Biotechnol Adv 2022; 60:108009. [PMID: 35738509 DOI: 10.1016/j.biotechadv.2022.108009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
Acceleration of chemical reactions by the enzymes optimized using protein engineering represents one of the key pillars of the contribution of biotechnology towards sustainability. Tunnels and channels of enzymes with buried active sites enable the exchange of ligands, ions, and water molecules between the outer environment and active site pockets. The efficient exchange of ligands is a fundamental process of biocatalysis. Therefore, enzymes have evolved a wide range of mechanisms for repetitive conformational changes that enable periodic opening and closing. Protein-ligand interactions are traditionally studied by molecular docking, whereas molecular dynamics is the method of choice for studying conformational changes and ligand transport. However, computational demands make molecular dynamics impractical for screening purposes. Thus, several approximative methods have been recently developed to study interactions between a protein and ligand during the ligand transport process. Apart from identifying the best binding modes, these methods also provide information on the energetics of the transport and identify problematic regions limiting the ligand passage. These methods use approximations to simulate binding or unbinding events rapidly (calculation times from minutes to hours) and provide energy profiles that can be used to rank ligands or pathways. Here we provide a critical comparison of available methods, showcase their results on sample systems, discuss their practical applications in molecular biotechnologies and outline possible future developments.
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Affiliation(s)
- Ondrej Vavra
- 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, Pekařská 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, Pekařská 53, 656 91 Brno, Czech Republic; Enantis, INBIT, Kamenice 34, 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, Pekařská 53, 656 91 Brno, Czech Republic.
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10
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Nguyen HL, Thai NQ, Li MS. Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution. J Chem Theory Comput 2022; 18:3860-3872. [PMID: 35512104 PMCID: PMC9202309 DOI: 10.1021/acs.jctc.1c01158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Steered molecular
dynamics (SMD) simulation is a powerful method
in computer-aided drug design as it can be used to access the relative
binding affinity with high precision but with low computational cost.
The success of SMD depends on the choice of the direction along which
the ligand is pulled from the receptor-binding site. In most simulations,
the unidirectional pathway was used, but in some cases, this choice
resulted in the ligand colliding with the complex surface of the exit
tunnel. To overcome this difficulty, several variants of SMD with
multidirectional pulling have been proposed, but they are not completely
devoid of disadvantages. Here, we have proposed to determine the direction
of pulling with a simple scoring function that minimizes the receptor–ligand
interaction, and an optimization algorithm called differential evolution
is used for energy minimization. The effectiveness of our protocol
was demonstrated by finding expulsion pathways of Huperzine A and
camphor from the binding site of Torpedo California acetylcholinesterase
and P450cam proteins, respectively, and comparing them with the previous
results obtained using memetic sampling and random acceleration molecular
dynamics. In addition, by applying this protocol to a set of ligands
bound with LSD1 (lysine specific demethylase 1), we obtained a much
higher correlation between the work of pulling force and experimental
data on the inhibition constant IC50 compared to that obtained using
the unidirectional approach based on minimal steric hindrance.
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Affiliation(s)
- Hoang Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.,Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 740500, Vietnam.,Vietnam National University, Ho Chi Minh City 71300, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap 81100, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland
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11
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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12
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Rydzewski J, Valsson O. Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling. J Phys Chem A 2021; 125:6286-6302. [PMID: 34213915 PMCID: PMC8389995 DOI: 10.1021/acs.jpca.1c02869] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Indexed: 12/29/2022]
Abstract
Machine learning methods provide a general framework for automatically finding and representing the essential characteristics of simulation data. This task is particularly crucial in enhanced sampling simulations. There we seek a few generalized degrees of freedom, referred to as collective variables (CVs), to represent and drive the sampling of the free energy landscape. In theory, these CVs should separate different metastable states and correspond to the slow degrees of freedom of the studied physical process. To this aim, we propose a new method that we call multiscale reweighted stochastic embedding (MRSE). Our work builds upon a parametric version of stochastic neighbor embedding. The technique automatically learns CVs that map a high-dimensional feature space to a low-dimensional latent space via a deep neural network. We introduce several new advancements to stochastic neighbor embedding methods that make MRSE especially suitable for enhanced sampling simulations: (1) weight-tempered random sampling as a landmark selection scheme to obtain training data sets that strike a balance between equilibrium representation and capturing important metastable states lying higher in free energy; (2) a multiscale representation of the high-dimensional feature space via a Gaussian mixture probability model; and (3) a reweighting procedure to account for training data from a biased probability distribution. We show that MRSE constructs low-dimensional CVs that can correctly characterize the different metastable states in three model systems: the Müller-Brown potential, alanine dipeptide, and alanine tetrapeptide.
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Affiliation(s)
- Jakub Rydzewski
- Institute
of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - Omar Valsson
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz D-55128, Germany
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13
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics 2020; 35:4986-4993. [PMID: 31077297 DOI: 10.1093/bioinformatics/btz386] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/11/2019] [Accepted: 05/05/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Filipovic
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - Jan Plhak
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Sergio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Ludek Matyska
- Institute of Computer Science, Masaryk University, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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15
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Lu C, Peng X, Lu D, Liu Z. Global and Kinetic Profiles of Substrate Diffusion in Candida antarctica Lipase B: Molecular Dynamics with the Markov-State Model. ACS OMEGA 2020; 5:9806-9812. [PMID: 32391467 PMCID: PMC7203684 DOI: 10.1021/acsomega.9b04432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Profiling substrate diffusion pathways with kinetic information, which accounts for the dynamic nature of enzyme-substrate interaction, can enable molecular reengineering of enzymes and process optimization of enzymatic catalysis. Candida antarctica lipase B (CALB) is extensively used for producing various chemicals because of its rich catalytic mechanisms, broad substrate spectrum, thermal stability, and tolerance to organic solvents. In this study, an all-atom molecular dynamics (MD) combined with Markov-state models (MSMs) implemented in pyEMMA was proposed to simulate diffusion pathways of 4-nitrophenyl ester (4NPE), a commonly used substrate, from the surface into the active site of CALB. Six important metastable conformations of CALB were identified in the diffusion process, including a closed state. An induced-fit mechanism incorporating multiple pathways with molecular information was proposed, which might find unprecedented applications for the rational design of lipase for green catalysis.
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Affiliation(s)
- Chenlin Lu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Xue Peng
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Diannan Lu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Zheng Liu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
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16
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Prasad K, Nikzad M, Sbarski I. Modeling Permeability in Multi-Phase Polymer Composites: A Critical Review of Semi-Empirical Approaches. POLYM REV 2020. [DOI: 10.1080/15583724.2020.1743306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- K. Prasad
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
| | - M. Nikzad
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
| | - I. Sbarski
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Australia
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17
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Ritacco I, Saltalamacchia A, Spinello A, Ippoliti E, Magistrato A. All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s. J Phys Chem Lett 2020; 11:1189-1193. [PMID: 31986051 DOI: 10.1021/acs.jpclett.9b03798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cytochromes P450 enzymes (CYP450s) promote the oxidative metabolism of a variety of substrates via the electrons supplied by the cytochrome P450 reductase (CPR) and upon formation of a CPR/CYP450 adduct. In spite of the pivotal regulatory importance of this process, the impact of CPR binding on the functional properties of its partner CYP450 remains elusive. By performing multiple microsecond-long all-atom molecular dynamics simulations of a 520 000-atom model of a CPR/CYP450 adduct embedded in a membrane mimic, we disclose the molecular terms for their interactions, considering the aromatase (HA) enzyme as a proxy of the CYP450 family. Our study strikingly unveils that CPR binding alters HA's functional motions, bolstering a change in the shape and type of the channels traveled by substrates/products during their access/egress to/from the enzyme's active site. Our outcomes unprecedentedly contribute to extricate the many entangled facets of the CYP450 metabolon, redrafting its intricate panorama from an atomic-level perspective.
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Affiliation(s)
- Ida Ritacco
- CNR-IOM c/o SISSA , via Bonomea 265 , 34136 Trieste , Italy
| | | | | | - Emiliano Ippoliti
- IAS-5/INM-9 Computational Biomedicine Institute and JARA-HPC , Forschungszentrum Jülich , Wilhelm-Johnen-Straße , 52425 Jülich , Germany
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18
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Bello M, Rodríguez-Fonseca RA, Correa-Basurto J. Complexation of peptide epitopes with G4-PAMAM dendrimer through ligand diffusion molecular dynamic simulations. J Mol Graph Model 2019; 96:107514. [PMID: 31877401 DOI: 10.1016/j.jmgm.2019.107514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/01/2022]
Abstract
Peptide epitopes from HIV-1 gp120 have been used to block the gp120-CD4 complex, whereas their poor absorbable or immunogenic properties prevent them from coupling to generation four polyamidoamine (PAMAM-G4) dendrimers. PAMAM-G4 are synthetic nanoparticles that are relatively nontoxic and nonimmunogenic have been employed as nanocarriers. In a previous study, two peptide epitopes (ABC and PGV04) from gp120 located at the protein-protein interface of the gp120-CD4 complex were identified through protein-protein dissociation. Then, their complexation with G4-PAMAM was evaluated through experimental and theoretical approaches, revealing a stoichiometry of 1:8/9 for G4-PAMAM and ABC or PGV04, respectively, providing important information that can be used to gain insight into the structural and energetic basis of the molecular binding of these G4-PAMAM-peptide systems. In this contribution, we performed ligand diffusion molecular dynamic simulations (LDMDSs) using 1.5 μs combined with the molecular mechanics generalized Born surface area (MMGBSA) approach, a strategy that successfully reproduced experimentally encapsulation on PAMAM-G4-ligand complexes, to explore the mechanism through which ABC and PGV04 are encapsulated by PAMAM-G4 under neutral and acid conditions. Our results reproduce the reported PAMAM-G4-peptide complex stoichiometry, revealing a slower peptide delivery at neutral conditions and a spontaneous release under acidic conditions. LDMDSs show that several peptides can reach stable G4-PAMAM complexes at neutral pH, and only a few are able to encapsulate on dendrimers without impacting dendrimer sphericity. Energetic analysis exploring different generalized Born models revealed that the ABC peptide has better binding properties than PGV04.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Diseño de fármacos y Bioinformática, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, 11340, Mexico.
| | - Rolando Alberto Rodríguez-Fonseca
- Laboratorio de Modelado Molecular, Diseño de fármacos y Bioinformática, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular, Diseño de fármacos y Bioinformática, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Ciudad de México, 11340, Mexico
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19
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Fischer A, Smieško M. Spontaneous Ligand Access Events to Membrane-Bound Cytochrome P450 2D6 Sampled at Atomic Resolution. Sci Rep 2019; 9:16411. [PMID: 31712722 PMCID: PMC6848145 DOI: 10.1038/s41598-019-52681-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
The membrane-anchored enzyme Cytochrome P450 2D6 (CYP2D6) is involved in the metabolism of around 25% of marketed drugs and its metabolic performance shows a high interindividual variation. While it was suggested that ligands access the buried active site of the enzyme from the membrane, no proof from unbiased simulations has been provided to support this hypothesis. Laboratory experiments fail to capture the access process which is suspected to influence binding kinetics. Here, we applied unbiased molecular dynamics (MD) simulations to investigate the access of ligands to wild-type CYP2D6, as well as the allelic variant CYP2D6*53. In multiple simulations, substrates accessed the active site of the enzyme from the protein-membrane interface to ultimately adopt a conformation that would allow a metabolic reaction. We propose the necessary steps for ligand access and the results suggest that the increased metabolic activity of CYP2D6*53 might be caused by a facilitated ligand uptake.
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Affiliation(s)
- André Fischer
- University of Basel, Department of Pharmaceutical Sciences, Basel, 4056, Switzerland
| | - Martin Smieško
- University of Basel, Department of Pharmaceutical Sciences, Basel, 4056, Switzerland.
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20
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Escalante DE, Aksan A. Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels. J Phys Chem B 2019; 123:6673-6685. [PMID: 31310534 DOI: 10.1021/acs.jpcb.9b03060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.
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Affiliation(s)
- Diego E Escalante
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Alptekin Aksan
- Department of Mechanical Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States.,BioTechnology Institute , University of Minnesota , St. Paul , Minnesota 55108 , United States
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21
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Escalante DE, Aksan A. Prediction of Ligand Transport along Hydrophobic Enzyme Nanochannels. Comput Struct Biotechnol J 2019; 17:757-760. [PMID: 31303980 PMCID: PMC6606821 DOI: 10.1016/j.csbj.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/08/2019] [Accepted: 06/01/2019] [Indexed: 12/22/2022] Open
Abstract
Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the model makes it applicable to any hydrophobic channel/ligand combination.
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Affiliation(s)
- Diego E. Escalante
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Alptekin Aksan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
- Corresponding author at: Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, United States.
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22
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Rydzewski J, Valsson O. Finding multiple reaction pathways of ligand unbinding. J Chem Phys 2019; 150:221101. [DOI: 10.1063/1.5108638] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87–100 Torun, Poland
| | - Omar Valsson
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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23
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Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations. Life (Basel) 2019; 9:life9020046. [PMID: 31167366 PMCID: PMC6617125 DOI: 10.3390/life9020046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.
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24
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Cuevas-Zuviría B, Garrido-Arandia M, Díaz-Perales A, Pacios LF. Energy Landscapes of Ligand Motion Inside the Tunnel-Like Cavity of Lipid Transfer Proteins: The Case of the Pru p 3 Allergen. Int J Mol Sci 2019; 20:ijms20061432. [PMID: 30901853 PMCID: PMC6471300 DOI: 10.3390/ijms20061432] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023] Open
Abstract
Allergies are a widespread problem in western countries, affecting a large part of the population, with levels of prevalence increasingly rising due to reasons still not understood. Evidence accumulated in recent years points to an essential role played by ligands of allergen proteins in the sensitization phase of allergies. In this regard, we recently identified the natural ligand of Pru p 3, a lipid transfer protein, a major allergen from peach fruit and a model of food allergy. The ligand of Pru p 3 has been shown to play a key role in the sensitization to peach and to other plant food sources that provoke cross-reactivity in a large proportion of patients allergic to peach. However, the question of which is the binding pose of this ligand in its carrier protein, and how it can be transferred to receptors of the immune system where it develops its function as a coadjuvant was not elucidated. In this work, different molecular dynamics simulations have been considered as starting points to study the properties of the ligand–protein system in solution. Besides, an energy landscape based on collective variables that describe the process of ligand motion within the cavity of Pru p 3 was obtained by using well-tempered metadynamics. The simulations revealed the differences between distinct binding modes, and also revealed important aspects of the motion of the ligand throughout its carrier protein, relevant to its binding–unbinding process. Our findings are potentially interesting for studying protein–ligand systems beyond the specific case of the allergen protein dealt with here.
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Affiliation(s)
- Bruno Cuevas-Zuviría
- Universidad Politécnica de Madrid (UPM), Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - María Garrido-Arandia
- Universidad Politécnica de Madrid (UPM), Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Araceli Díaz-Perales
- Universidad Politécnica de Madrid (UPM), Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, UPM, Ciudad Universitaria, 28040 Madrid, Spain.
| | - Luis F Pacios
- Universidad Politécnica de Madrid (UPM), Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, UPM, Ciudad Universitaria, 28040 Madrid, Spain.
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25
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Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophys J 2019. [PMID: 29539393 DOI: 10.1016/j.bpj.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.
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Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, Oregon.
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26
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Ciemny MP, Badaczewska-Dawid AE, Pikuzinska M, Kolinski A, Kmiecik S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int J Mol Sci 2019; 20:E606. [PMID: 30708941 PMCID: PMC6386871 DOI: 10.3390/ijms20030606] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling protein interactions, which involve disordered peptide partners or intrinsically disordered protein regions, and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein⁻peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein⁻peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution, and simulation of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | | | - Monika Pikuzinska
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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27
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Marques SM, Bednar D, Damborsky J. Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. Front Chem 2019; 6:650. [PMID: 30671430 PMCID: PMC6331733 DOI: 10.3389/fchem.2018.00650] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/13/2018] [Indexed: 12/28/2022] Open
Abstract
The computational prediction of unbinding rate constants is presently an emerging topic in drug design. However, the importance of predicting kinetic rates is not restricted to pharmaceutical applications. Many biotechnologically relevant enzymes have their efficiency limited by the binding of the substrates or the release of products. While aiming at improving the ability of our model enzyme haloalkane dehalogenase DhaA to degrade the persistent anthropogenic pollutant 1,2,3-trichloropropane (TCP), the DhaA31 mutant was discovered. This variant had a 32-fold improvement of the catalytic rate toward TCP, but the catalysis became rate-limited by the release of the 2,3-dichloropropan-1-ol (DCP) product from its buried active site. Here we present a computational study to estimate the unbinding rates of the products from DhaA and DhaA31. The metadynamics and adaptive sampling methods were used to predict the relative order of kinetic rates in the different systems, while the absolute values depended significantly on the conditions used (method, force field, and water model). Free energy calculations provided the energetic landscape of the unbinding process. A detailed analysis of the structural and energetic bottlenecks allowed the identification of the residues playing a key role during the release of DCP from DhaA31 via the main access tunnel. Some of these hot-spots could also be identified by the fast CaverDock tool for predicting the transport of ligands through tunnels. Targeting those hot-spots by mutagenesis should improve the unbinding rates of the DCP product and the overall catalytic efficiency with TCP.
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Affiliation(s)
- Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
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28
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Zhou H, Wang F, Tao P. t-Distributed Stochastic Neighbor Embedding Method with the Least Information Loss for Macromolecular Simulations. J Chem Theory Comput 2018; 14:5499-5510. [PMID: 30252473 PMCID: PMC6679899 DOI: 10.1021/acs.jctc.8b00652] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Dimensionality reduction methods are usually applied on molecular dynamics simulations of macromolecules for analysis and visualization purposes. It is normally desired that suitable dimensionality reduction methods could clearly distinguish functionally important states with different conformations for the systems of interest. However, common dimensionality reduction methods for macromolecules simulations, including predefined order parameters and collective variables (CVs), principal component analysis (PCA), and time-structure based independent component analysis (t-ICA), only have limited success due to significant key structural information loss. Here, we introduced the t-distributed stochastic neighbor embedding (t-SNE) method as a dimensionality reduction method with minimum structural information loss widely used in bioinformatics for analyses of macromolecules, especially biomacromolecules simulations. It is demonstrated that both one-dimensional (1D) and two-dimensional (2D) models of the t-SNE method are superior to distinguish important functional states of a model allosteric protein system for free energy and mechanistic analysis. Projections of the model protein simulations onto 1D and 2D t-SNE surfaces provide both clear visual cues and quantitative information, which is not readily available using other methods, regarding the transition mechanism between two important functional states of this protein.
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Affiliation(s)
- Hongyu Zhou
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Feng Wang
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
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29
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Kouza M, Banerji A, Kolinski A, Buhimschi I, Kloczkowski A. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes. Molecules 2018; 23:molecules23081995. [PMID: 30103417 PMCID: PMC6222447 DOI: 10.3390/molecules23081995] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/25/2022] Open
Abstract
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Correspondence: ; Tel.: +48-22-55-26-364
| | - Anirban Banerji
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Irina Buhimschi
- Center for Perinatal Research, Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA;
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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30
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Wilding M, Scott C, Warden AC. Computer-Guided Surface Engineering for Enzyme Improvement. Sci Rep 2018; 8:11998. [PMID: 30097591 PMCID: PMC6086876 DOI: 10.1038/s41598-018-30434-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 11/12/2022] Open
Abstract
Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and its immediate vicinity, while the remainder of the protein is something of an enigma. Studying highly homologous transaminases with strictly conserved active sites, but different substrate preferences and activities, we predict and experimentally validate that the surface of the protein far from the active site carries out a decisive role in substrate selectivity and catalytic efficiency. Using a unique molecular dynamics approach and novel trajectory analysis, we demonstrate the phenomenon of surface-directed ligand diffusion in this well-known protein family for the first time. Further, we identify the residues involved in directing substrate, design surface channel variants endowed for improved kinetic properties and establish a broadly applicable new approach for protein engineering.
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Affiliation(s)
- Matthew Wilding
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia
- Research School of Chemistry, Australian National University, Building 137 Sullivan's Creek Road, Canberra, ACT 2601, Australia
| | - Colin Scott
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Andrew C Warden
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia.
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31
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Filipe HAL, Javanainen M, Salvador A, Galvão AM, Vattulainen I, Loura LMS, Moreno MJ. Quantitative Assessment of Methods Used To Obtain Rate Constants from Molecular Dynamics Simulations—Translocation of Cholesterol across Lipid Bilayers. J Chem Theory Comput 2018; 14:3840-3848. [DOI: 10.1021/acs.jctc.8b00150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hugo A. L. Filipe
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, P-3004-517 Coimbra, Portugal
| | - Matti Javanainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Armindo Salvador
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, P-3004-517 Coimbra, Portugal
| | - Adelino M. Galvão
- CQE—Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1049-001 Lisboa, Portugal
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
- MEMPHYS—Center
for Biomembrane Physics, FI-00014 Helsinki, Finland
| | - Luís M. S. Loura
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, P-3000-548 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra Chemistry Center, University of Coimbra, P-3004-535 Coimbra, Portugal
- Chemistry Department, University of Coimbra, P-3004-535 Coimbra, Portugal
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32
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Rydzewski J, Jakubowski R, Nowak W, Grubmüller H. Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways. J Chem Theory Comput 2018; 14:2843-2851. [PMID: 29715428 DOI: 10.1021/acs.jctc.8b00173] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 μs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.
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Affiliation(s)
- J Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - R Jakubowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland.,Centre of New Technologies, University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland
| | - W Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - H Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany
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33
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Rydzewski J, Nowak W. Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning. J Chem Phys 2018; 148:115101. [DOI: 10.1063/1.5013659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- J. Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - W. Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
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34
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Rare-event sampling in ligand diffusion. Phys Life Rev 2017; 22-23:85-87. [DOI: 10.1016/j.plrev.2017.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 08/27/2017] [Indexed: 01/06/2023]
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35
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Kuczera K. Finding optimal paths through biomolecular mazes: Comment on: "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by J. Rydzewski and W. Nowak. Phys Life Rev 2017; 22-23:77-78. [PMID: 28797667 DOI: 10.1016/j.plrev.2017.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS 66045, United States.
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36
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Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations. Sci Rep 2017; 7:7736. [PMID: 28798338 PMCID: PMC5552751 DOI: 10.1038/s41598-017-07993-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/05/2017] [Indexed: 01/12/2023] Open
Abstract
Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
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37
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Li MS. Ligand migration and steered molecular dynamics in drug discovery: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak. Phys Life Rev 2017; 22-23:79-81. [PMID: 28807592 DOI: 10.1016/j.plrev.2017.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Lotnikow 32/46, 02-668 Warsaw, Poland.
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38
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Magistrato A. Direct in silico visualization of ligands channelling through proteins: The next-generation frontier of computational biology: Comment on 'Ligand diffusion via enhanced sampling molecular dynamics' by Jakub Rydzewski and Wieslaw Nowak. Phys Life Rev 2017; 22-23:82-84. [PMID: 28818495 DOI: 10.1016/j.plrev.2017.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Alessandra Magistrato
- CNR-IOM-Democritos c/o, International School for Advanced Studies (SISSA), Via Bonomea 265, 34135, Trieste, Italy.
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39
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Toward more efficient simulations of slow processes in large biomolecular systems: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak. Phys Life Rev 2017; 22-23:75-76. [PMID: 28781239 DOI: 10.1016/j.plrev.2017.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022]
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40
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Marques SM, Dunajova Z, Prokop Z, Chaloupkova R, Brezovsky J, Damborsky J. Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. J Chem Inf Model 2017; 57:1970-1989. [PMID: 28696117 DOI: 10.1021/acs.jcim.7b00070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the SN2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust strategies in the development of new biocatalysts.
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Affiliation(s)
- Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Zuzana Dunajova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital Brno , Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 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 Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University , Kamenice 5/A13, 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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41
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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42
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Magistrato A, Sgrignani J, Krause R, Cavalli A. Single or Multiple Access Channels to the CYP450s Active Site? An Answer from Free Energy Simulations of the Human Aromatase Enzyme. J Phys Chem Lett 2017; 8:2036-2042. [PMID: 28423275 DOI: 10.1021/acs.jpclett.7b00697] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cytochromes P450 (CYP450s), in particular, CYP19A1 and CYP17A1, are key clinical targets of breast and prostate anticancer therapies, critical players in drug metabolism, and their overexpression in tumors is associated with drug resistance. In these enzymes, ligand (substrates, drugs) metabolism occurs in deeply buried active sites accessible only via several grueling channels, whose exact biological role remains unclear. Gaining direct insights on the mechanism by which ligands travel in and out is becoming increasingly important given that channels are involved in the modulation of binding/dissociation kinetics and the specificity of ligands toward a CYP450. This has profound implications for enzymatic efficiency and drug efficacy/toxicity. Here, by applying free energy methods, for a cumulative simulation time of 20 μs, we provide detailed atomistic characterization and free energy profiles of the entry/exit routes preferentially followed by a substrate (androstenedione) and a last-generation inhibitor (letrozole) to/from the catalytic site of CYP19A1 (the human aromatase (HA) enzyme), a key clinical target against breast cancer, studied here as prototypical CYP450. Despite the remarkably different size/shape/hydrophobicity of the ligands, two channels appear accessible to their entrance, while only one exit route appears to be preferential. Our study shows that the preferential paths may be conserved among different CYP450s. Moreover, our results highlight that, at least in the case of HA, ligand channeling is associated with large enzyme structural rearrangements. A wise choice of the computational method and very long simulations are, thus, required to obtain fully converged quantitative free energy profiles, which might be used to design novel biocatalysts or next-generation cytochrome inhibitors with an in silico tuned Km.
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Affiliation(s)
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI) , Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Rolf Krause
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana (USI) , Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI) , Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
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