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Park H, Patel P, Haas R, Huerta EA. APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. Proc Natl Acad Sci U S A 2024; 121:e2311888121. [PMID: 38913887 DOI: 10.1073/pnas.2311888121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/25/2023] [Indexed: 06/26/2024] Open
Abstract
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.
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Affiliation(s)
- Hyun Park
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parth Patel
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Roland Haas
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - E A Huerta
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, The University of Chicago, Chicago, IL 60637
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Selvam B, Paul A, Yu YC, Chen LQ, Shukla D. SWEET family transporters act as water conducting carrier proteins in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.23.600272. [PMID: 38979333 PMCID: PMC11230166 DOI: 10.1101/2024.06.23.600272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Dedicated water channels are involved in the facilitated diffusion of water molecules across the cell membrane in plants. Transporter proteins are also known to transport water molecules along with substrates, however the molecular mechanism of water permeation is not well understood in plant transporters. Here, we show plant sugar transporters from the SWEET ( S ugar W ill E ventually be E xported T ransporter) family act as water-conducting carrier proteins via a variety of passive and active mechanisms that allow diffusion of water molecules from one side of the membrane to the other. This study provides a molecular perspective on how plant membrane transporters act as water carrier proteins, a topic that has not been extensively explored in literature. Water permeation in membrane transporters could occur via four distinct mechanisms which form our hypothesis for water transport in SWEETs. These hypothesis are tested using molecular dynamics simulations of the outward-facing, occluded, and inward-facing state of AtSWEET1 to identify the water permeation pathways and the flux associated with them. The hydrophobic gates at the center of the transport tunnel act as a barrier that restricts water permeation. We have performed in silico single and double mutations of the hydrophobic gate residues to examine the changes in the water conductivity. Surprisingly, the double mutant allows the water permeation to the intracellular half of the membrane and forms a continuous water channel. These computational results are validated by experimentally examining the transport of hydrogen peroxide molecules by the AtSWEET family of transporters. We have also shown that the transport of hydrogen peroxide follows the similar mechanism as water transport in AtSWEET1. Finally, we conclude that similar water-conduction states are also present in other SWEET transporters due to the high sequence and structure conservation exhibited by this transporter family.
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Selvam B, Chiang N, Shukla D. Energetics of substrate transport in proton-dependent oligopeptide transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592129. [PMID: 38746282 PMCID: PMC11092630 DOI: 10.1101/2024.05.01.592129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The PepT So transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepT So in different states, the molecular basis of peptide recognition and transport by PepT So is not fully elucidated. In this study, we employed molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepT So transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. Furthermore, we elucidated the proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepT So and identify critical residues that facilitate transport.
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Vaughan RA, Henry LK, Foster JD, Brown CR. Post-translational mechanisms in psychostimulant-induced neurotransmitter efflux. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2024; 99:1-33. [PMID: 38467478 DOI: 10.1016/bs.apha.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The availability of monoamine neurotransmitters in the brain is under the control of dopamine, norepinephrine, and serotonin transporters expressed on the plasma membrane of monoaminergic neurons. By regulating transmitter levels these proteins mediate crucial functions including cognition, attention, and reward, and dysregulation of their activity is linked to mood and psychiatric disorders of these systems. Amphetamine-based transporter substrates stimulate non-exocytotic transmitter efflux that induces psychomotor stimulation, addiction, altered mood, hallucinations, and psychosis, thus constituting a major component of drug neurochemical and behavioral outcomes. Efflux is under the control of transporter post-translational modifications that synergize with other regulatory events, and this review will summarize our knowledge of these processes and their role in drug mechanisms.
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Affiliation(s)
- Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Christopher R Brown
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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Paul A, Shukla D. Oligomerization of Monoamine Transporters. Subcell Biochem 2024; 104:119-137. [PMID: 38963486 DOI: 10.1007/978-3-031-58843-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Transporters of the monoamine transporter (MAT) family regulate the uptake of important neurotransmitters like dopamine, serotonin, and norepinephrine. The MAT family functions using the electrochemical gradient of ions across the membrane and comprises three transporters, dopamine transporter (DAT), serotonin transporter (SERT), and norepinephrine transporter (NET). MAT transporters have been observed to exist in monomeric states to higher-order oligomeric states. Structural features, allosteric modulation, and lipid environment regulate the oligomerization of MAT transporters. NET and SERT oligomerization are regulated by levels of PIP2 present in the membrane. The kink present in TM12 in the MAT family is crucial for dimer interface formation. Allosteric modulation in the dimer interface hinders dimer formation. Oligomerization also influences the transporters' function, trafficking, and regulation. This chapter will focus on recent studies on monoamine transporters and discuss the factors affecting their oligomerization and its impact on their function.
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Affiliation(s)
- Arnav Paul
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Center for Biophysics and Quantitative Biology, Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Chen J, Shukla D. Effect of histidine covalent modification on strigolactone receptor activation and selectivity. Biophys J 2023; 122:1219-1228. [PMID: 36798027 PMCID: PMC10111262 DOI: 10.1016/j.bpj.2023.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/17/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The parasitic weed Striga has led to billions of dollars' worth of agricultural productivity loss worldwide. Striga detects host plants using compounds of the strigolactone class of phytohormones. Early steps in the strigolactone signaling pathway involve substrate binding and hydrolysis followed by a conformational change to an "active" or "closed" state, after which it associates with a MAX2-family downstream signaling partner. The structures of the inactive and active states of strigolactone receptors are known through X-ray crystallography, and the transition pathway from the inactive to active state in apo receptors has previously been characterized using molecular dynamics simulations. However, it also has been suggested that a covalent butenolide modification of the receptor on the catalytic histidine through substrate hydrolysis promotes formation of the active state. Using molecular dynamics simulations, we show that the presence of the covalent butenolide enhances activation in both AtD14, a receptor found in Arabidopsis, and ShHTL7, a receptor found in Striga, but the enhancement is ∼50 times greater in ShHTL7. We also show that several conserved interactions with the covalent butenolide modification promote transition to the active state in both AtD14 (non-parasite) and ShHTL7 (parasite). Finally, we demonstrate that the enhanced activation of ShHTL7 likely results from disruption of ShHTL7-specific histidine interactions that inhibited activation in the apo case. These results provide a possible explanation for difference in strigolactone sensitivity seen between different strigolactone-sensitive proteins and can be used to aid the design of selective modulators to control Striga parasites.
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Affiliation(s)
- Jiming Chen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois; Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois.
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Yang W, Zhuang J, Li C, Cheng GJ. Unveiling the Methyl Transfer Mechanisms in the Epigenetic Machinery DNMT3A-3L: A Comprehensive Study Integrating Assembly Dynamics with Catalytic Reactions. Comput Struct Biotechnol J 2023; 21:2086-2099. [PMID: 36968013 PMCID: PMC10034213 DOI: 10.1016/j.csbj.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023] Open
Abstract
In epigenetic mechanisms, DNA methyltransferase 3 alpha (DNMT3A) acts as an initiator for DNA methylation and prevents the downstream genes from expressing. Perturbations of DNMT3A functions may cause uncontrolled gene expression, resulting in pathogenic consequences such as cancers. It is, therefore, vitally important to understand the catalytic process of DNMT3A in its biological macromolecule assembly, viz., heterotetramer: (DNMT3A-3 L)dimer. In this study, we utilized molecular dynamics (MD) simulations, Markov State Models (MSM), and quantum mechanics/molecular mechanics simulations (QM/MM) to investigate the de novo methyl transfer process. We identified the dynamics of the key residues relevant to the insertion of the target cytosine (dC) into the catalytic domain of DNMT3A, and the detailed potential energy surface of the seven-step reaction referring to methyl transfer. Our calculated potential energy barrier (22.51 kcal/mol) approximates the former experimental data (23.12 kcal/mol). The conformational change of the 5-methyl-cytosine (5mC) intermediate was found necessary in forming a four-water chain for the elimination step, which is unique to the other DNMTs. The biological assembly facilitates the creation of such a water chain, and the elimination occurs in an asynchronized mechanism in the two catalytic pockets. We anticipate the findings can enable a better understanding of the general mechanisms of the de novo methyl transfer for fulfilling the key enzymatic functions in epigenetics. And the unique elimination of DNMT3A might ignite novel methods for designing anti-cancer and tumor inhibitors of DNMTs.
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Affiliation(s)
- Wei Yang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Biotechnology, University of Science and Technology of China, Hefei 230026, China
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jingyuan Zhuang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Gui-Juan Cheng
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Key Laboratory of Steroid Drug Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Corresponding author at: Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Sk MF, Kar P. Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus kinase via multiscale simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:833-859. [PMID: 36398489 DOI: 10.1080/1062936x.2022.2145352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The Janus kinase (JAK) is a master regulator of the JAK/STAT pathway. Dysregulation of this signalling cascade causes neuroinflammation and autoimmune disorders. Therefore, JAKs have been characterized as an attractive target for developing anti-inflammatory drugs. Nowadays, designing efficient, effective, and specific targeted therapeutics without being cytotoxic has gained interest. We performed the virtual screening of natural products in combination with pharmacological analyses. Subsequently, we performed molecular dynamics simulations to study the stability of the ligand-bound complexes and ligand-induced inactive conformations. Notably, inactive kinases display remarkable conformational plasticity; however, ligand-induced molecular mechanisms of these conformations are still poorly understood. Herein, we performed a free energy landscape analysis to explore the conformational plasticity of the JAK1 kinase. Leonurine, STOCK1N-68642, STOCK1N-82656, and STOCK1N-85809 bound JAK1 exhibited a smooth transition from an active (αC-in) to a completely inactive conformation (αC-out). Ligand binding induces disorders in the αC-helix. Molecular mechanics Poisson Boltzmann surface area (MM/PBSA) calculation suggested three phytochemicals, namely STOCK1N-68642, Epicatechin, and STOCK1N-98615, have higher binding affinity compared to other ligand molecules. The ligand-induced conformational plasticity revealed by our simulations differs significantly from the available crystal structures, which might help in designing allosteric drugs.
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Affiliation(s)
- M F Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, India
| | - P Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, India
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Horne J, Shukla D. Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering. Ind Eng Chem Res 2022; 61:6235-6245. [DOI: 10.1021/acs.iecr.1c04943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jesse Horne
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Bioengineering, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Department of Plant Biology, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana−Champaign, Champaign, Illinois 61801, United States
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