101
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Ratnasinghe BD, Haque N, Wagenknecht JB, Jensen DR, Esparza GV, Leverence EN, De Assuncao TM, Mathison AJ, Lomberk G, Smith BC, Volkman BF, Urrutia R, Zimmermann MT. Beyond Structural Bioinformatics for Genomics with Dynamics Characterization of an Expanded KRAS Mutational Landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.536249. [PMID: 37207265 PMCID: PMC10189839 DOI: 10.1101/2023.04.28.536249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Current capabilities in genomic sequencing outpace functional interpretations. Our previous work showed that 3D protein structure calculations enhance mechanistic understanding of genetic variation in sequenced tumors and patients with rare diseases. The KRAS GTPase is among the critical genetic factors driving cancer and germline conditions. Because KRAS-altered tumors frequently harbor one of three classic hotspot mutations, nearly all studies have focused on these mutations, leaving significant functional ambiguity across the broader KRAS genomic landscape observed in cancer and non-cancer diseases. Herein, we extend structural bioinformatics with molecular simulations to study an expanded landscape of 86 KRAS mutations. We identify multiple coordinated changes strongly associated with experimentally established KRAS biophysical and biochemical properties. The patterns we observe span hotspot and non-hotspot alterations, which can all dysregulate Switch regions, producing mutation-restricted conformations with different effector binding propensities. We experimentally measured mutation thermostability and identified shared and distinct patterns with simulations. Our results indicate mutation-specific conformations which show potential for future research into how these alterations reverberate into different molecular and cellular functions. The data we present is not predictable using current genomic tools, demonstrating the added functional information derived from molecular simulations for interpreting human genetic variation.
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Affiliation(s)
- Brian D. Ratnasinghe
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Neshatul Haque
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jessica B. Wagenknecht
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Davin R. Jensen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Guadalupe V. Esparza
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elise N. Leverence
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Thiago Milech De Assuncao
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela J. Mathison
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Gwen Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian C. Smith
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian F. Volkman
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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102
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Zhang X, Li X, Wang Y, Zhang X, Liu Y. Computational Study of the Fe(II) and α-Ketoglutarate-Dependent Aryloxyalkanoate Dioxygenase (AAD-1) in the Degradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid. J Chem Inf Model 2023; 63:2759-2768. [PMID: 37100030 DOI: 10.1021/acs.jcim.2c01381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The AAD-1 enzyme belongs to the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent nonheme aryloxyalkanoate dioxygenase family (AADs), which catalyzes the breakdown of 2,4-dichlorophenoxyacetic acid (2,4-D, an active ingredient of thousands of commercial herbicides) by using the highly active Fe(IV)═O complex. Multiple species of bacteria degrade 2,4-D via a pathway initiated by AADs; however, the detail of how they promote the cleavage of the ether C-O bond to generate 2,4-dichlorophenol (2,4-DCP) and glyoxylate is still unclear, which is the prerequisite for the further degradation of these halogenated aromatics. In this work, based on the crystal structure of AAD-1, the computational models were constructed, and a series of QM/MM and QM-only calculations were performed to explore the cleavage of the ether bond in 2,4-D with the catalysis of AAD-1. Our calculations reveal that AAD-1 may be only responsible for the hydroxylation of the substrate to generate the intermediate hemiacetal, which corresponds to an overall energy barrier of 14.2 kcal/mol on the quintet state surface, and the decomposition of the hemiacetal in the active site center of AAD-1 was calculated to be rather slow, corresponding to an energy barrier of 24.5 kcal/mol. In contrast, the decomposition of the free hemiacetal molecule in a solvent was calculated to be quite easy. Whether the decomposition of the hemiacetal occurs inside or outside the activation site is still worthy of experimental verification.
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Affiliation(s)
- Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xianghui Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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103
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Freites JA, Louis MN, Tobias DJ. Insights into the solubility of γ $$ \gamma $$ D-crystallin from multiscale atomistic simulations. J Comput Chem 2023. [PMID: 37093714 DOI: 10.1002/jcc.27116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
The molecular basis underlying the rich phase behavior of globular proteins remains poorly understood. We use atomistic multiscale molecular simulations to model the solution-state conformational dynamics and interprotein interactions of γ $$ \gamma $$ D-crystallin and its P23T-R36S mutant, which drastically limits the protein solubility, at both infinite dilution and at a concentration where the mutant fluid phase and crystalline phase coexist. We find that while the mutant conserves the protein fold, changes to the surface exposure of residues in the neighborhood of residue-36 enhance protein-protein interactions and develop specific protein-protein contacts found in the protein crystal lattice.
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Affiliation(s)
- J Alfredo Freites
- Department of Chemistry, University of California, Irvine, California, USA
| | - Mohab N Louis
- Department of Chemistry, University of California, Irvine, California, USA
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, California, USA
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104
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Yuan Y, Wang F. Dipole Cooperativity and Polarization Frustration Determine the Secondary Structure Distribution of Short Alanine Peptides in Water. J Phys Chem B 2023; 127:3126-3138. [PMID: 36848625 PMCID: PMC10108861 DOI: 10.1021/acs.jpcb.2c07947] [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: 11/11/2022] [Revised: 02/16/2023] [Indexed: 03/01/2023]
Abstract
The physical driving forces for secondary structure preferences of hydrated alanine peptide are investigated with B3LYP-D3(BJ) and the adaptive force matching (AFM) method. The AFM fit to the DFT surface, ALA2022, provides excellent agreement with the nuclear magnetic resonance scalar coupling constants from experiments. In turn, the model is used to gain insight into the physical driving forces behind secondary structure preferences of hydrated peptides. DFT calculations with and without the Conductor-like Screening Model (COSMO) show that the α helix is stabilized by solvent polarization due to dipole cooperativity. The two adjacent amide groups in β strand form a near-planar trapezoid that is not much larger than the size of water molecules. When the finite size of a water molecule is considered, the stabilization from solvent polarization for such a trapezoid is frustrated. Water molecules cannot find orientations to properly stabilize all four polar regions close to each other with such an awkward arrangement. This leads to quite substantial reduction in polarization stabilization. Although the polyproline II (PP-II) conformation is very similar to the β strand, the small twist in the backbone angles allowed much improved polarization stabilization. The improved polarization, when combined with favorable intrapeptide interactions, leads to the PP-II to be lowest in free energy. Other factors, such as the entropic TΔS and the ϕ, ψ coupling terms, are also studied but are found to play only a minor role. The insight shown in this work helps to better understand the structure of globular and intrinsic disordered proteins and facilitate future force field development.
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Affiliation(s)
- Ying Yuan
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Wang
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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105
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Chen D, Bali S, Singh R, Wosztyl A, Mullapudi V, Vaquer-Alicea J, Jayan P, Melhem S, Seelaar H, van Swieten JC, Diamond MI, Joachimiak LA. FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation. Nat Commun 2023; 14:1625. [PMID: 36959205 PMCID: PMC10036635 DOI: 10.1038/s41467-023-37274-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Amyloid deposition of the microtubule-associated protein tau is associated with neurodegenerative diseases. In frontotemporal dementia with abnormal tau (FTD-tau), missense mutations in tau enhance its aggregation propensity. Here we describe the structural mechanism for how an FTD-tau S320F mutation drives spontaneous aggregation, integrating data from in vitro, in silico and cellular experiments. We find that S320F stabilizes a local hydrophobic cluster which allosterically exposes the 306VQIVYK311 amyloid motif; identify a suppressor mutation that destabilizes S320F-based hydrophobic clustering reversing the phenotype in vitro and in cells; and computationally engineer spontaneously aggregating tau sequences through optimizing nonpolar clusters surrounding the S320 position. We uncover a mechanism for regulating tau aggregation which balances local nonpolar contacts with long-range interactions that sequester amyloid motifs. Understanding this process may permit control of tau aggregation into structural polymorphs to aid the design of reagents targeting disease-specific tau conformations.
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Affiliation(s)
- Dailu Chen
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ruhar Singh
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Aleksandra Wosztyl
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Parvathy Jayan
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shamiram Melhem
- Department of Neurology & Alzheimer Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Harro Seelaar
- Department of Neurology & Alzheimer Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - John C van Swieten
- Department of Neurology & Alzheimer Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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106
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Banerjee A, Dutt M. A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly. J Chem Phys 2023; 158:114105. [PMID: 36948821 DOI: 10.1063/5.0138510] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Protein mimics such as peptoids form self-assembled nanostructures whose shape and function are governed by the side chain chemistry and secondary structure. Experiments have shown that a peptoid sequence with a helical secondary structure assembles into microspheres that are stable under various conditions. The conformation and organization of the peptoids within the assemblies remains unknown and is elucidated in this study via a hybrid, bottom-up coarse-graining approach. The resultant coarse-grained (CG) model preserves the chemical and structural details that are critical for capturing the secondary structure of the peptoid. The CG model accurately captures the overall conformation and solvation of the peptoids in an aqueous solution. Furthermore, the model resolves the assembly of multiple peptoids into a hemispherical aggregate that is in qualitative agreement with the corresponding results from experiments. The mildly hydrophilic peptoid residues are placed along the curved interface of the aggregate. The composition of the residues on the exterior of the aggregate is determined by two conformations adopted by the peptoid chains. Hence, the CG model simultaneously captures sequence-specific features and the assembly of a large number of peptoids. This multiscale, multiresolution coarse-graining approach could help in predicting the organization and packing of other tunable oligomeric sequences of relevance to biomedicine and electronics.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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107
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Liu RR, Zhai HL, Zhu M, Shao HP, Wang TH. Inhibitory mechanism of n-MTAB AuNPs for α-synuclein aggregation. J Mol Model 2023; 29:103. [PMID: 36944862 DOI: 10.1007/s00894-023-05513-8] [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: 06/30/2022] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
OBJECTIVE The aggregation of alpha-synuclein (α-syn) is closely related to the pathogenesis and dysfunction of Parkinson's disease. METHODS To investigate the potential of nanoparticlemediated therapy, the interactive mechanism between α-syn and n-myristyltrimethylammonium bromide (MTAB) Gold nanoparticles (AuNPs) with different diameters was explored by molecular dynamics simulations. RESULTS The results indicated that there was a directional interaction between α-syn and n-MTAB AuNPs, in which the driving force for the binding of the C-terminus in α-syn came from electrostatic interactions and the nonamyloid β component (NAC) domain exhibited weak hydrophobic interactions as well as electrostatic interaction, thereby preventing α-syn aggregation. Energy statistics and analysis showed that for 5-MTAB AuNPs, acidic amino acids such as Glu and Asp played a very important role. CONCLUSIONS This study not only demonstrated a theoretical foundation for the behavior of biomolecules directionally adsorbed on the surface of biofunctional nanoparticles but also indicated that 5-MTAB AuNPs may be a potential inhibitor against α-syn protein aggregation.
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Affiliation(s)
- Rui Rui Liu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Hong Lin Zhai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
| | - Min Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Hai Ping Shao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Tian Hua Wang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
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108
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Yue Z, Li C, Voth GA. The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter. Biophys J 2023; 122:1068-1085. [PMID: 36698313 PMCID: PMC10111279 DOI: 10.1016/j.bpj.2023.01.025] [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: 10/24/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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109
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Iwasa M, Takeda S, Narita A, Maéda Y, Oda T. Mutagenic analysis of actin reveals the mechanism of His161 flipping that triggers ATP hydrolysis. Front Cell Dev Biol 2023; 11:1105460. [PMID: 37009486 PMCID: PMC10062479 DOI: 10.3389/fcell.2023.1105460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
The dynamic assembly of actin is controlled by the hydrolysis of ATP, bound to the center of the molecule. Upon polymerization, actin undergoes a conformational change from the monomeric G-form to the fibrous F-form, which is associated with the flipping of the side chain of His161 toward ATP. His161 flipping from the gauche-minus to gauche-plus conformation leads to a rearrangement of the active site water molecules, including ATP attacking water (W1), into an orientation capable of hydrolysis. We previously showed that by using a human cardiac muscle α-actin expression system, mutations in the Pro-rich loop residues (A108G and P109A) and in a residue that was hydrogen-bonded to W1 (Q137A) affect the rate of polymerization and ATP hydrolysis. Here, we report the crystal structures of the three mutant actins bound to AMPPNP or ADP-Pi determined at a resolution of 1.35–1.55 Å, which are stabilized in the F-form conformation with the aid of the fragmin F1 domain. In A108G, His161 remained non-flipped despite the global actin conformation adopting the F-form, demonstrating that the side chain of His161 is flipped to avoid a steric clash with the methyl group of A108. Because of the non-flipped His161, W1 was located away from ATP, similar to G-actin, which was accompanied by incomplete hydrolysis. In P109A, the absence of the bulky proline ring allowed His161 to be positioned near the Pro-rich loop, with a minor influence on ATPase activity. In Q137A, two water molecules replaced the side-chain oxygen and nitrogen of Gln137 almost exactly at their positions; consequently, the active site structure, including the W1 position, is essentially conserved. This seemingly contradictory observation to the reported low ATPase activity of the Q137A filament could be attributed to a high fluctuation of the active site water. Together, our results suggest that the elaborate structural design of the active site residues ensures the precise control of the ATPase activity of actin.
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Affiliation(s)
- Mitsusada Iwasa
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Shuichi Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
- *Correspondence: Toshiro Oda, ; Shuichi Takeda,
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuichiro Maéda
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Toshiro Oda
- Faculty of Health and Welfare, Tokai Gakuin University, Kakamigahara, Japan
- *Correspondence: Toshiro Oda, ; Shuichi Takeda,
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110
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Zhang Y, Liu X, Chen J. Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations. J Chem Theory Comput 2023; 19:1602-1614. [PMID: 36791464 PMCID: PMC10795075 DOI: 10.1021/acs.jctc.2c01139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.
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Affiliation(s)
- Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaorong Liu
- Corresponding Authors: (XL), (JC), Phone: (413) 545-3386 (JC)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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111
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Maruyama Y, Igarashi R, Ushiku Y, Mitsutake A. Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation. J Chem Inf Model 2023; 63:1529-1541. [PMID: 36821519 PMCID: PMC10015464 DOI: 10.1021/acs.jcim.2c01444] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
We apply moving root-mean-square deviation (mRMSD), which does not require a reference structure, as a method for analyzing protein dynamics. This method can be used to calculate the root-mean-square deviation (RMSD) of structure between two specified time points and to analyze protein dynamics behavior through time series analysis. We applied this method to the Trp-cage trajectory calculated by the Anton supercomputer and found that it shows regions of stable states as well as the conventional RMSD. In addition, we extracted a characteristic structure in which the side chains of Asp1 and Arg16 form hydrogen bonds near the most stable structure of the Trp-cage. We also determined that ≥20 ns is an appropriate time interval to investigate protein dynamics using mRMSD. Applying this method to NuG2 protein, we found that mRMSD can be used to detect regions of metastable states in addition to the stable state. This method can be applied to molecular dynamics simulations of proteins whose stable structures are unknown.
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Affiliation(s)
- Yutaka Maruyama
- OMRON SINIC X Corporation, Tokyo 113-0033, Japan.,Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Ryo Igarashi
- OMRON SINIC X Corporation, Tokyo 113-0033, Japan
| | | | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
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112
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Dulko-Smith B, Ojeda-May P, Ådén J, Wolf-Watz M, Nam K. Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. J Chem Inf Model 2023; 63:1556-1569. [PMID: 36802243 DOI: 10.1021/acs.jcim.2c01629] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme's conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme's function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK's conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme's conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme's active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.
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Affiliation(s)
- Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Pedro Ojeda-May
- High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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113
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Chen B, Mansour B, Zheng E, Liu Y, Gauld JW, Wang Q. Fundamentals behind the specificity of Cysteinyl-tRNA synthetase: MD and QM/MM joint investigations. Proteins 2023; 91:354-362. [PMID: 36196751 DOI: 10.1002/prot.26433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Cysteinyl-tRNA synthetase (CysRS) catalyzes the aminoacylation reaction of cysteine to its cognate tRNACys in the first step of protein translation. It is found that CysRS is different from other aaRSs as it transfers cysteine without the need for an editing reaction, which is not applicable in the case of serine despite the similarity in their structures. Surprisingly, the reasons why CysRS has high amino acid specificity are not clear yet. In this research, the binding configurations of Cys-AMP and its near-cognate amino acid Ser-AMP with CysRS are compared by Molecular Dynamics (MD). The results reveal that CysRS screens the substrate Cys-AMP to a certain extent in the process of combination and recognition, thus providing a guarantee for the high selectivity of the next reaction. While Ser-AMP is in a folded state in CysRS. In the meanwhile, the interaction between Cys-AMP and Zn963 in CysRS is much stronger than Ser-AMP. The substrate-assisted aminoacylation mechanism in CysRS is also explored by Quantum Mechanics/Molecular Mechanics (QM/MM) modeling. According to the QM/MM potential energies, the energy barrier of TSCys-AMP is 91.75 kJ/mol, while that of TSSer-AMP is close to 150 kJ/mol. Based on thermochemistry calculations, it is found that the product of Cys-AMP is more stable than the reactant. In contrast, Ser-AMP has a reactant that is more stable than its product. As a result, it reflects that the specificity of CysRS originates from both the kinetic and thermodynamical perspectives of the reaction. Our investigations demonstrate comprehensively on how CysRS recognizes and catalyzes the substrate Cys-AMP, hoping to provide some guidance for researchers in this area.
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Affiliation(s)
- Binbin Chen
- Department of Chemistry, Zhejiang University, Hangzhou, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Basel Mansour
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - En Zheng
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Yingchun Liu
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Canada
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou, China
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114
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Chaudhary M, Nain V, Sehgal D. Molecular docking and dynamic simulation analysis of Hepatitis E virus protease in complexing with the E64 inhibitor. J Biomol Struct Dyn 2023; 41:1342-1350. [PMID: 34931595 DOI: 10.1080/07391102.2021.2019124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The unavailability of a suitable treatment for human Hepatitis E virus (HEV) infection necessitate the development of anti HEV drugs. The HEV papain-like cysteine proteases (HEV PCP) is a crucial target to prevent viral replication and progression. E64 is a known HEV PCP inhibitor; however, its molecular mechanism of inhibition is not yet known. Since the crystal structure of HEV PCP is not available, the primary focuses of the present study was to refine the predicted HEV PCP structural model by molecular dynamics (MD) simulation. Further, we performed a 200 ns MD simulation to understand the structural complexity of HEV PCP and the effect of E64 binding with HEV PCP. The E64 binding with active site residues Gln48, Thr51, Gln55, Cys52, Ser81, Gln 98, Cys 132, Arg158, His159, Asn 160 and Ala96 leads to reduced fluctuations in the residue at N-terminal (18-41) that include the CHC motif (26-28). However, most of the other non interacting residues, including the inter-domain linker region (46-87), showed increased fluctuations in the HEV PCP-E64 complex. The residue Asp21 and Ala96 are involved in the formation of interdomain interactions in the HEV PCP apo enzyme. While in the PCP-E64 complex, E64 binds to Ala96 and creates a steric hindrance to prevent interdomain interactions. Thus, the E64 binding reduces interdomain interactions and restrict domain movements in the HEV PCP-E64 complex. This information will be important for the chemically designing more effective derivatives of E64 developing HEV PCP specific inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meenakshi Chaudhary
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
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115
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Dong L, Liu Y. Catalytic Mechanism of Pyridoxal 5'-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study. J Chem Inf Model 2023; 63:1313-1322. [PMID: 36745546 DOI: 10.1021/acs.jcim.2c01593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aminodeoxychorismate lyase (ADCL) is a kind of pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate (PABA), which is a key step for the biosynthesis of folate. To illuminate the reaction details at the atomistic level, an enzyme-substrate reactant model has been constructed, and QM/MM calculations have been performed. Our calculation results reveal that the overall catalytic cycle contains 11 elementary steps, which can be described by three stages, including the transamination reaction of PLP, the release of pyruvate and aromatization of ADC, and the recovery to the initial aldimine. During the reaction, a series of intramolecular proton transfer are involved, which are the key for the C-N bond formation and cleavage as well as the aromatization of the ADC ring. In addition to forming the Schiff base with the pocket residue Lys251 and substrate in the internal aldimine and the external aldimine, respectively, the coenzyme PLP also plays a critical role in the intramolecular proton transfer by employing its hydroxyl oxygen anion and phosphate group. These findings may provide useful information for further understanding the catalytic mechanism of other PLP-dependent enzymes.
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Affiliation(s)
- Lihua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, Shandong 250013, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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116
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Seo B, Savoie BM. Evidence That Less Can Be More for Transferable Force Fields. J Chem Inf Model 2023; 63:1188-1195. [PMID: 36744744 DOI: 10.1021/acs.jcim.2c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Graph-based parameter assignment has been the basis for developing transferable force fields for molecular dynamics simulations for decades. Nevertheless, transferable force fields vary in how specifically terms are defined with respect to the molecular graph and the procedures for generating parametrization data. More-specific force-field terms increase the complexity of the force field, theoretically increasing accuracy but also increasing training data requirements. In contrast, less-specific force fields can be reused across larger regions of chemical space, theoretically reducing accuracy but also reducing the number of parameters and training data requirements. Here, the tradeoffs between force-field specificity and accuracy are quantified by parametrizing three new sets of force fields with varying levels of graph specificity, using a shared procedure for generating training data. These force fields are benchmarked for their ability to reproduce the structural features and liquid properties of 87 organic molecules at 146 distinct state points. The overall accuracy for properties that were directly trained on rapidly saturates as the graph specificity of the force-field increases. From this, we conclude there is at best a marginal benefit of using less transferable and more complex force fields with common sources of quantum-chemically derived training data. When looking at properties unseen during training, there is some evidence that the more-complex force fields even perform slightly worse. These results are rationalized by the fortuitous regularization of force fields based on less-specific and more-transferable atom types. Both the saturation in the accuracy of training properties and the marginally worse performance on off-target properties fundamentally contradict the expectation that bespoke force fields are generally more accurate, given their larger number of parameters, and suggests that increasing force-field complexity should be carefully justified against performance gains and balanced against available training data.
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Affiliation(s)
- Bumjoon Seo
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana47906, United States
| | - Brett M Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana47906, United States
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117
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Rebolledo-Bustillo M, Garcia-Gomez D, Dávila EM, Castro ME, Caballero NA, Melendez FJ, Baizabal-Aguirre VM, Sanchez-Gaytan BL, Perez-Aguilar JM. Structural Basis of the Binding Mode of the Antineoplastic Compound Motixafortide (BL-8040) in the CXCR4 Chemokine Receptor. Int J Mol Sci 2023; 24:ijms24054393. [PMID: 36901829 PMCID: PMC10001991 DOI: 10.3390/ijms24054393] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 02/25/2023] Open
Abstract
Modulation of the CXCL12-CXCR4 signaling axis is of the utmost importance due to its central involvement in several pathological disorders, including inflammatory diseases and cancer. Among the different currently available drugs that inhibit CXCR4 activation, motixafortide-a best-in-class antagonist of this GPCR receptor-has exhibited promising results in preclinical studies of pancreatic, breast, and lung cancers. However, detailed information on the interaction mechanism of motixafortide is still lacking. Here, we characterize the motixafortide/CXCR4 and CXCL12/CXCR4 protein complexes by using computational techniques including unbiased all-atom molecular dynamics simulations. Our microsecond-long simulations of the protein systems indicate that the agonist triggers changes associated with active-like GPCR conformations, while the antagonist favors inactive conformations of CXCR4. Detailed ligand-protein analysis indicates the importance of motixafortide's six cationic residues, all of which established charge-charge interactions with acidic CXCR4 residues. Furthermore, two synthetic bulky chemical moieties of motixafortide work in tandem to restrict the conformations of important residues associated with CXCR4 activation. Our results not only elucidate the molecular mechanism by which motixafortide interacts with the CXCR4 receptor and stabilizes its inactive states, but also provide essential information to rationally design CXCR4 inhibitors that preserve the outstanding pharmacological features of motixafortide.
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Affiliation(s)
- Mariana Rebolledo-Bustillo
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - David Garcia-Gomez
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Eliud Morales Dávila
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - María Eugenia Castro
- Chemistry Center, Science Institute, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Norma A. Caballero
- School of Biological Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Francisco J. Melendez
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Victor M. Baizabal-Aguirre
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Km. 9.5 s/n Carretera Morelia-Zinapécuaro, La Palma, Tarímbaro, Morelia 58893, MICH, Mexico
| | - Brenda L. Sanchez-Gaytan
- Chemistry Center, Science Institute, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
- Correspondence: ; Tel.: +52-(222)-2295500 (ext. 4089)
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118
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Khairnar S, Sonawane A, Cheke RS, Kharkar PS, Gaikwad V, Patil S, Aware V. Hit discovery of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines as potential anti-glioblastoma therapeutics: Design, synthesis, biological evaluation, and computational screening. Drug Dev Res 2023; 84:561-578. [PMID: 36823756 DOI: 10.1002/ddr.22046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/15/2023] [Accepted: 01/28/2023] [Indexed: 02/25/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly-aggressive, dreadful disease with poor prognosis and disappointing clinical success. There is an unmet medical need of molecularly-targeted therapeutics for GBM treatment. In the present work, a series of novel 2-phenyl-substituted 4-amino-6,7-dihydro-5H-cyclopenta[d]pyrimidines was designed, synthesized, purified, characterized, and evaluated for cytotoxicity against glioblastoma cell line U87-MG. The design process (virtual library enumeration around the core, physicochemical and molecular property prediction/calculation of the designs, filtering the undesirable ones, and the diversity analyses of the lead-like designs), was carefully curated so as to obtain a set of structurally-diverse, novel molecules (total 20), with a particular focus on the relatively unexplored core structure, 6,7-dihydro-5H-cyclopenta[d]pyrimidine. The preliminary screening was done using MTT assay at 10 and 100 μM concentrations of the title compounds F1 -F20 and positive control cisplatin, which yielded six hits (% inhibition at 10 μM: ~50%)-F2 , F3 , F5 , F7 , F15 , and F20 , which were taken up for IC50 determination. The top hits F2 and F7 (IC50 < 10 μM) were further used for computational studies such as target prediction, followed by their molecular docking in the binding sites of the top-3 predicted targets (epidermal growth factor receptor kinase domain, cyclin-dependent kinase 2 [CDK2]) /cyclin E, and anaplastic lymphoma kinase [ALK]). The docking pose analyses revealed interesting trends. The relatively planar core structure, presence of favorable hinge-binding substructures, basic groups, all added up, and culminated in appreciable cytotoxicity against GBM cell line.
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Affiliation(s)
- Sanjay Khairnar
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India.,Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Anjali Sonawane
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Rameshwar S Cheke
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Vishwas Gaikwad
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Sambhaji Patil
- Department of Chemistry, Organic Chemistry Research Centre, K. R. T. Arts, B. H. Commerce and A. M. Science College, Nashik, India
| | - Valmik Aware
- Department of Chemistry, SNJB's KKHA Arts, SMGL Commerce and SPHJ Science College, Chandwad, India
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119
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Abdel-Gawad WM, Abdelmohsen M, Gaber MH, Khalil WMA, Abu-Elmagd MSM. Molecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride. J Biomol Struct Dyn 2023; 41:13891-13901. [PMID: 36812302 DOI: 10.1080/07391102.2023.2183040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
The one-microsecond molecular dynamics simulations of a membrane-protein complex investigate the influence of the aqueous sodium chloride solutions on the structure and dynamics of a palmitoyl-oleoyl-phosphatidylcholine bilayer membrane. The simulations were performed on five different concentrations (40, 150, 200, 300, and 400 mM) in addition to a salt-free system by using the charmm36 force field for all atoms. Four biophysical parameters, (membrane thicknesses of annular and bulk lipids, and the area per lipid of both leaflets), were computed separately. Nevertheless, the area per lipid was expressed by using the Voronoi algorithm. All time-independent analyses were carried out for the last 400 ns trajectories. Different concentrations revealed dissimilar membrane dynamics before equilibration. The biophysical properties of the membrane (thickness, area-per-lipid, and order parameter) have non-significant changes with increasing ionic strength, however, the 150 mM system had exceptional behavior. Sodium cations were dynamically penetrating the membrane forming weak coordinate bonds with single or multiple lipids. Nevertheless, the binding constant was unaffected by the cation concentration. The electrostatic and Van der Waals energies of lipid-lipid interactions were influenced by the ionic strength. On the other hand, the Fast Fourier Transform was performed to figure out the dynamics at the membrane-protein interface. The nonbonding energies of membrane-protein interactions and order parameters explained the differences in the synchronization pattern. All results were consensus with experimental and theoretical works.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mahmoud Abdelmohsen
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Mathematics and Engineering Physics Department, The Higher Institute of Engineering, Shorouk Academy, El-Shorouk City, Cairo, Egypt
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120
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Pulkkinen LIA, Barrass SV, Lindgren M, Pace H, Överby AK, Anastasina M, Bally M, Lundmark R, Butcher SJ. Simultaneous membrane and RNA binding by tick-borne encephalitis virus capsid protein. PLoS Pathog 2023; 19:e1011125. [PMID: 36787339 PMCID: PMC9970071 DOI: 10.1371/journal.ppat.1011125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/27/2023] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate the interactions of the wild-type and truncated capsid proteins with membranes with biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids, which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane.
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Affiliation(s)
- Lauri Ilmari Aurelius Pulkkinen
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sarah Victoria Barrass
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Marie Lindgren
- Department of Clinical Microbiology, Faculty of Medicine, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Hudson Pace
- Department of Clinical Microbiology, Faculty of Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Anna K. Överby
- Department of Clinical Microbiology, Faculty of Medicine, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Maria Anastasina
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Marta Bally
- Department of Clinical Microbiology, Faculty of Medicine, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Richard Lundmark
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Department of Integrative Medical Biology, Faculty of Medicine, Umeå University, Umeå, Sweden
- * E-mail: (SJB); (RL)
| | - Sarah Jane Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- * E-mail: (SJB); (RL)
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121
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Guseva DV, Glagolev MK, Lazutin AA, Vasilevskaya VV. Revealing Structural and Physical Properties of Polylactide: What Simulation Can Do beyond the Experimental Methods. POLYM REV 2023. [DOI: 10.1080/15583724.2023.2174136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- D. V. Guseva
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - M. K. Glagolev
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - A. A. Lazutin
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - V. V. Vasilevskaya
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
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122
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Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists. Pharmaceutics 2023; 15:pharmaceutics15020527. [PMID: 36839848 PMCID: PMC9962304 DOI: 10.3390/pharmaceutics15020527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Selective antiadhesion antagonists of Uropathogenic Escherichia coli (UPEC) type-1 Fimbrial adhesin (FimH) are attractive alternatives for antibiotic therapies and prophylaxes against acute or recurrent urinary tract infections (UTIs) caused by UPECs. A rational small library of FimH antagonists based on previously described C-linked allyl α-D-mannopyranoside was synthesized using Heck cross-coupling reaction using a series of iodoaryl derivatives. This work reports two new members of FimH antagonist amongst the above family with sub nanomolar affinity. The resulting hydrophobic aglycones, including constrained alkene and aryl groups, were designed to provide additional favorable binding interactions with the so-called FimH "tyrosine gate". The newly synthesized C-linked glycomimetic antagonists, having a hydrolytically stable anomeric linkage, exhibited improved binding when compared to previously published analogs, as demonstrated by affinity measurement through interactions by FimH lectin. The crystal structure of FimH co-crystallized with one of the nanomolar antagonists revealed the binding mode of this inhibitor into the active site of the tyrosine gate. In addition, selected mannopyranoside constructs neither affected bacterial growth or cell viability nor interfered with antibiotic activity. C-linked mannoside antagonists were effective in decreasing bacterial adhesion to human bladder epithelial cells (HTB-9). Therefore, these molecules constituted additional therapeutic candidates' worth further development in the search for potent anti-adhesive drugs against infections caused by UPEC.
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123
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Chiariello M, Grünewald F, Zarmiento-Garcia R, Marrink SJ. pH-Dependent Conformational Switch Impacts Stability of the PsbS Dimer. J Phys Chem Lett 2023; 14:905-911. [PMID: 36662680 PMCID: PMC9900633 DOI: 10.1021/acs.jpclett.2c03760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
The photosystem II PsbS protein triggers the photoprotective mechanism of plants by sensing the acidification of the thylakoid lumen. Despite the mechanism of action of PsbS would require a pH-dependent monomerization of the dimeric form, a clear connection between the pH-induced structural changes and the dimer stability is missing. Here, by applying constant pH coarse-grained and all-atom molecular dynamics simulations, we investigate the pH-dependent structural response of the PsbS dimer. We find that the pH variation leads to structural changes in the lumen-exposed helices, located at the dimeric interface, providing an effective switch between PsbS inactive and active form. Moreover, the monomerization free energies reveal that in the neutral pH conformation, where the network of H-bond interactions at the dimeric interface is destroyed, the protein-protein interaction is weaker. Our results show how the pH-dependent conformations of PsbS affect their dimerization propensity, which is at the basis of the photoprotective mechanism.
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Affiliation(s)
| | | | - Rubi Zarmiento-Garcia
- Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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Baréa P, Yamazaki DADS, Lima DDS, Seixas FAV, da Costa WF, Gauze GDF, Sarragiotto MH. Design, synthesis, molecular docking and biological evaluation of β-carboline derivatives as cholinesterase inhibitors. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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125
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Kumar S, Rao NNS, Reddy KSSVP, Padole MC, Deshpande PA. Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis. Phys Chem Chem Phys 2023; 25:3472-3484. [PMID: 36637052 DOI: 10.1039/d2cp05406j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Orotate phosphoribosyltransferase (OPRT) catalyses the reversible phosphoribosyl transfer from α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to orotic acid (OA) to yield orotidine 5'-monophosphate (OMP) during the de novo synthesis of nucleotides. Numerous studies have reported the inhibition of this reaction as a strategy to check diseases like tuberculosis, malaria and cancer. Insight into the inhibition of this reaction is, therefore, of urgent interest. In this study, we implemented a QM/MM framework on OPRT derived from Saccharomyces cerevisiae to obtain insights into the competitive binding of OA and OA-mimetic inhibitors by quantifying their interactions with OPRT. 4-Hydroxy-6-methylpyridin-2(1H) one showed the best inhibiting activity among the structurally similar OA-mimetic inhibitors, as quantified from the binding energetics. Our analysis of protein-ligand interactions unveiled the association of this inhibitory ligand with a strong network of hydrogen bonds, a large contribution of hydrophobic contacts, and bridging water molecules in the binding site. The ortho-substituted CH3 group in the compound resulted in a large population of π-electrons in the aromatic ring of this inhibitor, supporting the ligand binding further.
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Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - N N Subrahmanyeswara Rao
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - K S S V Prasad Reddy
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Manjusha C Padole
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Parag A Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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Rosales-Hernández MC, Bello M, Toledano JV, Feregrino BCE, Correa Basurto J, Fragoso Morales LG, Torres-Ramos MA. Molecular dynamics simulations depict structural motions of the whole human aryl hydrocarbon receptor influencing its binding of ligands and HSP90. J Biomol Struct Dyn 2023; 41:13138-13153. [PMID: 36705144 DOI: 10.1080/07391102.2023.2171132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/15/2023] [Indexed: 01/28/2023]
Abstract
The aryl hydrocarbon receptor (AhR) has broad biological functions when its ligands activate it; the non-binding interactions with AhR have not been fully elucidated due to the absence of a complete tridimensional (3D) structure. Therefore, utilization of the whole 3D structure from Homo sapiens AhR by in silico studies will allow us to better study and analyze the binding mode of its full and partial agonists, and antagonists, as well as its interaction with the HSP90 chaperone. The 3D AhR structure was obtained from I-TASSER and subjected to molecular dynamics (MD) simulations to obtain different structural conformations and determine the most populated AhR conformer by clustering analyses. The AhR-3D structures selected from MD simulations and those from clustering analyses were used to achieve docking studies with some of its ligands and protein-protein docking with HSP90. Once the AhR-3D structure was built, its Ramachandran maps and energy showed a well-qualified 3D model. MD simulations showed that the per-Arnt-Sim homology (PAS) PAS A, PAS B, and Q domains underwent conformational changes, identifying the conformation when agonists were binding also, and HSP90 was binding near the PAS A, PAS B, and Q domains. However, when antagonists are binding, HSP90 does not bind near the PAS A, PAS B, and Q domains. These studies show that the complex agonist-AhR-HSP90 can be formed, but this complex is not formed when an antagonist is binding. Knowing the conformations when the ligands bind to AHR and the behavior of HSP90 allows for an understanding of its activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Jazziel Velazquez Toledano
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Barbara Citlali Escudero Feregrino
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
- Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Mexico City, México
| | - José Correa Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Seccion de Estudios de Posgrado. Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, México City, Mexico
| | - Leticia Guadalupe Fragoso Morales
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrago e Investigación. Escuela Superior de Medicina, Instituto Politécnico Nacional. Plan de San Luis y Díaz Mirón s/n, Ciudad de México, Mexico
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127
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Andrews B, Ruggiero T, Urbanc B. How do salt and lipids affect conformational dynamics of Aβ42 monomers in water? Phys Chem Chem Phys 2023; 25:2566-2583. [PMID: 36602150 DOI: 10.1039/d2cp05044g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is well established that amyloid β-protein (Aβ) self-assembly is involved in triggering of Alzheimer's disease. On the other hand, evidence of physiological function of Aβ interacting with lipids has only begun to emerge. Details of Aβ-lipid interactions, which may underlie physiological and pathological activities of Aβ, are not well understood. Here, the effects of salt and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids on conformational dynamics of Aβ42 monomer in water are examined by all-atom molecular dynamics (MD). We acquired six sets of 250 ns long MD trajectories for each of the three lipid concentrations (0, 27, and 109 mM) in the absence and presence of 150 mM salt. Ten replica trajectories per set are used to enhance sampling of Aβ42 conformational space. We show that salt facilitates long-range tertiary contacts in Aβ42, resulting in more compact Aβ42 conformations. By contrast, addition of lipids results in lipid-concentration dependent Aβ42 unfolding concomitant with enhanced stability of the turn in the A21-A30 region. At the high lipid concentration, salt enables the N-terminal region of Aβ42 to form long-range tertiary contacts and interact with lipids, which results in formation of a parallel β-strand. Aβ42 forms stable lipid-protein complexes whereby the protein is adhered to the lipid cluster rather than embedded into it. We propose that the inability of Aβ42 monomer to get embedded into the lipid cluster may be important for facilitating repair of leaks in the blood-brain barrier without penetrating and damaging cellular membranes.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Thomas Ruggiero
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
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128
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de Araujo IG, Pattaro-Júnior JR, Barbosa CG, Philippsen GS, Silva AR, Ioshino RS, Moraes CB, Freitas-Junior LH, Barros L, Peralta RM, Fernandez MA, Seixas FAV. Potential of plant extracts in targeting SARS-CoV-2 main protease: an in vitro and in silico study. J Biomol Struct Dyn 2023; 41:12204-12213. [PMID: 36651196 DOI: 10.1080/07391102.2023.2166589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/01/2023] [Indexed: 01/19/2023]
Abstract
The deaths caused by the covid-19 pandemic have recently decreased due to a worldwide effort in vaccination campaigns. However, even vaccinated people can develop a severe form of the disease that requires ICU admission. As a result, the search for antiviral drugs to treat these severe cases has become a necessity. In this context, natural products are an interesting alternative to synthetic medicines used in drug repositioning, as they have been consumed for a long time through traditional medicine. Many natural compounds found in plant extracts have already been shown to be effective in treating viral and bacterial diseases, making them possible hits to exploit against covid-19. The objective of this work was to evaluate the antiviral activity of different plant extracts available in the library of natural products of the Universidade Estadual de Maringá, by inhibiting the SARS-CoV-2 main protease (Mpro), and by preventing viral infection in a cellular model. As a result, the extract of Cytinus hypocistis, obtained by ultrasound, showed a Mpro inhibition capacity greater than 90%. In the infection model assays using Vero cells, an inhibition of 99.6% was observed, with a selectivity index of 42.7. The in silico molecular docking simulations using the extract compounds against Mpro, suggested Tellimagrandin II as the component of C. hypocistis extract most likely to inhibit the viral enzyme. These results demonstrate the potential of C. hypocistis extract as a promising source of natural compounds with antiviral activity against covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Cecilia Gomes Barbosa
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Universidade Municipal de São Caetano do Sul (USCS), São Caetano, Brazil
- Bela Vista, São Paulo, Brazil
| | | | - Ana Rita Silva
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha, (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, CIETUS-IBSAL, Universidad de Salamanca, Salamanca, España
| | | | | | | | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha, (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | | | - Maria Aparecida Fernandez
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Maringá, P.R. Brazil
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129
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Ji X, Liu H, Zhang Y, Chen J, Chen HF. Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. J Chem Inf Model 2023; 63:362-374. [PMID: 36533639 DOI: 10.1021/acs.jcim.2c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabetes, and other diseases. Experimental methods can hardly capture the ensemble of diverse conformations for IDPs. Molecular dynamics (MD) simulations can sample continuous conformations that might provide a valuable complement to experimental data. However, the accuracy of MD simulations depends on the quality of force field. In particular, the evolutionary conservation and coevolution of IDPs introduce that current force fields could not precisely reproduce the conformation of IDPs. In order to improve the performance of force field, deep learning and reweighting methods were used to automatically generate personal force field parameters for intrinsically disordered and ordered proteins. At first, the deep learning method predicted more accuracy φ/ψ dihedral of residue than the previous method. Then, reweighting optimized the personal force field parameters for each residue. Finally, typical representative systems such as IDPs, structure protein, and fast-folding protein were used to evaluate this force field. The results indicate that two personal force field parameters (named PPFF1 and PPFF1_af2) could better reproduce the experimental observables than ff03CMAP force field. In summary, this strategy will provide feasibility for the development of precise personal force fields.
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Affiliation(s)
- Xiaoyue Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jun Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China.,Shanghai Center for Bioinformation Technology, Shanghai200235, China
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130
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Yamashita T. Molecular Dynamics Simulation for Investigating Antigen-Antibody Interaction. Methods Mol Biol 2023; 2552:101-107. [PMID: 36346587 DOI: 10.1007/978-1-0716-2609-2_4] [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: 06/16/2023]
Abstract
Molecular dynamics (MD) simulation is a computational method which elucidates the protein dynamics. Following analyses characterize the dynamics and structural change as well as interaction energy. To characterize the protein structure effectively, the internal angular coordinates are often useful. Directional analysis provides the averages and variances of those coordinates in a mathematically rigorous way. Here, we describe not only a standard MD simulation procedure for the antigen-antibody system but also an umbrella sampling method following a multistep targeted MD simulation (US/mTMD), which is useful for evaluating the free energy profile along the antigen-antibody dissociation coordinate.
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Affiliation(s)
- Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
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131
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Frantz MC, Rozot R, Marrot L. NRF2 in dermo-cosmetic: From scientific knowledge to skin care products. Biofactors 2023; 49:32-61. [PMID: 36258295 DOI: 10.1002/biof.1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022]
Abstract
The skin is the organ that is most susceptible to the impact of the exposome. Located at the interface with the external environment, it protects internal organs through the barrier function of the epidermis. It must adapt to the consequences of the harmful effects of solar radiation, the various chemical constituents of atmospheric pollution, and wounds associated with mechanical damage: oxidation, cytotoxicity, inflammation, and so forth. In this biological context, a capacity to adapt to the various stresses caused by the exposome is essential; otherwise, more or less serious conditions may develop accelerated aging, pigmentation disorders, atopy, psoriasis, and skin cancers. Nrf2-controlled pathways play a key role at this level. Nrf2 is a transcription factor that controls genes involved in oxidative stress protection and detoxification of chemicals. Its involvement in UV protection, reduction of inflammation in processes associated with healing, epidermal differentiation for barrier function, and hair regrowth, has been demonstrated. The modulation of Nrf2 in the skin may therefore constitute a skin protection or care strategy for certain dermatological stresses and disorders initiated or aggravated by the exposome. Nrf2 inducers can act through different modes of action. Keap1-dependent mechanisms include modification of the cysteine residues of Keap1 by (pro)electrophiles or prooxidants, and disruption of the Keap1-Nrf2 complex. Indirect mechanisms are suggested for numerous phytochemicals, acting on upstream pathways, or via hormesis. While developing novel and safe Nrf2 modulators for skin care may be challenging, new avenues can arise from natural compounds-based molecular modeling and emerging concepts such as epigenetic regulation.
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Affiliation(s)
| | - Roger Rozot
- Advanced Research, L'OREAL Research & Innovation, Aulnay-sous-Bois, France
| | - Laurent Marrot
- Advanced Research, L'OREAL Research & Innovation, Aulnay-sous-Bois, France
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132
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Chiba S, Okuno Y, Ohta M. Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations. Methods Mol Biol 2023; 2552:323-331. [PMID: 36346601 DOI: 10.1007/978-1-0716-2609-2_18] [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: 06/16/2023]
Abstract
Structure-based site-directed affinity maturation of antibodies can be expanded by multiple-point mutations to obtain various mutants. However, selecting the appropriate number of promising mutants for experimental evaluation from the vast number of combinations of multiple-point mutations is challenging. In this report, we describe how to narrow candidate mutants using the so-called weak interaction analysis such as CH-π and CH-O in addition to widely recognized interactions such as hydrogen bonds.
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Affiliation(s)
- Shuntaro Chiba
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masateru Ohta
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan.
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133
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ElSawy KM, Alminderej FM, Caves LSD. Disruption of 3CLpro protease self-association by short peptides as a potential route to broad spectrum coronavirus inhibitors. J Biomol Struct Dyn 2022; 40:13901-13911. [PMID: 34720051 DOI: 10.1080/07391102.2021.1996462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coronaviruses have posed a persistent threat to human health over the last two decades. Despite the accumulated knowledge about coronavirus-related pathogens, development of an effective treatment for its new variant COVID-19 is highly challenging. For the highly-conserved and main coronavirus protease 3CLpro, dimerization is known to be essential for its catalytic activity and thereby for virus proliferation. Here, we assess the potential of short peptide segments to disrupt dimerization of the 3CLpro protease as a route to block COVID-19 proliferation. Based on the X-ray structure of the 3CLpro dimer, we identified the SPSGVY126QCAMRP dodecapeptide segment as overlapping the hotspot regions on the 3CLpro dimer interface. Using computational blind docking of the peptide to the 3CLpro monomer, we found that the SPSGVY126QCAMRP peptide has favourable thermodynamic binding (ΔG= -5.93 kcal/mol) to the hotspot regions at the 3CLpro dimer interface. Importantly, the peptide was also found to preferentially bind to the hotspot regions compared to other potential binding sites lying away from the dimer interface (ΔΔG=-1.31 kcal/mol). Docking of peptides corresponding to systematic mutation of the V125 and Y126 residues led to the identification of seven peptides, SPSGHAQCAMRP, SPSGVTQCAMRP, SPSGKPQCAMRP, SPSGATQCAMRP, SPSGWLQCAMRP, SPSGAPQCAMRP and SPSGHPQCAMRP, that outperform the wild-type SPSGVY126QCAMRP peptide in terms of preferential binding to the 3CLpro dimer interface. These peptides have the potential to disrupt 3CLpro dimerization and therefore could provide lead structures for the development of broad spectrum COVID-19 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia.,York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK
| | - Fahad M Alminderej
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia
| | - Leo S D Caves
- York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK.,Independent Researcher, São Felix da Marinha, Portugal
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134
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Ahmed S, Mahtarin R, Islam MS, Das S, Al Mamun A, Ahmed SS, Ali MA. Remdesivir analogs against SARS-CoV-2 RNA-dependent RNA polymerase. J Biomol Struct Dyn 2022; 40:11111-11124. [PMID: 34315339 DOI: 10.1080/07391102.2021.1955743] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has already taken many lives but is still continuing its spread and exerting jeopardizing effects. This study is aimed to find the most potent ligands from 703 analogs of remdesivir against RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus . RdRp is a major part of a multi-subunit transcription complex of the virus, which is essential for viral replication. In clinical trials, it has been found that remdesivir is effective to inhibit viral replication in Ebola and in primary human lung cell cultures; it effectively impedes replication of a broad-spectrum pre-pandemic bat coronaviruses and epidemic human coronaviruses. After virtual screening, 30 most potent ligands and remdesivir were modified with triphosphate. Quantum mechanics-based quantitative structure-activity relationship envisages the binding energy for ligands applying partial least square (PLS) regression. PLS regression remarkably predicts the binding energy of the effective ligands with an accuracy of 80% compared to the value attained from molecular docking. Two ligands (L4:58059550 and L28:126719083), which have more interactions with the target protein than the other ligands including standard remdesivir triphosphate, were selected for further analysis. Molecular dynamics simulation is done to assess the stability and dynamic nature of the drug-protein complex. Binding-free energy results via PRODIGY server and molecular mechanics/Poisson-Boltzmann surface area method depict that the potential and solvation energies play a crucial role. Considering all computational analysis, we recommend the best remdesivir analogs can be utilized for efficacy test through in vitro and in vivo trials against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sinthyia Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Shamiul Islam
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Susmita Das
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Sayeda Samina Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
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135
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Govorunova EG, Sineshchekov OA, Brown LS, Bondar AN, Spudich JL. Structural Foundations of Potassium Selectivity in Channelrhodopsins. mBio 2022; 13:e0303922. [PMID: 36413022 PMCID: PMC9765531 DOI: 10.1128/mbio.03039-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Potassium-selective channelrhodopsins (KCRs) are light-gated K+ channels recently found in the stramenopile protist Hyphochytrium catenoides. When expressed in neurons, KCRs enable high-precision optical inhibition of spiking (optogenetic silencing). KCRs are capable of discriminating K+ from Na+ without the conventional K+ selectivity filter found in classical K+ channels. The genome of H. catenoides also encodes a third paralog that is more permeable for Na+ than for K+. To identify structural motifs responsible for the unusual K+ selectivity of KCRs, we systematically analyzed a series of chimeras and mutants of this protein. We found that mutations of three critical residues in the paralog convert its Na+-selective channel into a K+-selective one. Our characterization of homologous proteins from other protists (Colponema vietnamica, Cafeteria burkhardae, and Chromera velia) and metagenomic samples confirmed the importance of these residues for K+ selectivity. We also show that Trp102 and Asp116, conserved in all three H. catenoides paralogs, are necessary, although not sufficient, for K+ selectivity. Our results provide the foundation for further engineering of KCRs for optogenetic needs. IMPORTANCE Recently discovered microbial light-gated ion channels (channelrhodopsins) with a higher permeability for K+ than for Na+ (potassium-selective channelrhodopsins [kalium channelrhodopsins, or KCRs]) demonstrate an alternative K+ selectivity mechanism, unrelated to well-characterized "selectivity filters" of voltage- and ligand-gated K+ channels. KCRs can be used for optogenetic inhibition of neuronal firing and potentially for the development of gene therapies to treat neurological and cardiovascular disorders. In this study, we identified structural motifs that determine the K+ selectivity of KCRs that provide the foundation for their further improvement as optogenetic tools.
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Affiliation(s)
- Elena G. Govorunova
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Oleg A. Sineshchekov
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Leonid S. Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Bucharest, Romania
- Institute of Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
| | - John L. Spudich
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
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136
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Baatallah N, Elbahnsi A, Chevalier B, Castanier S, Mornon JP, Pranke I, Edelman A, Sermet-Gaudelus I, Callebaut I, Hinzpeter A. Acting on the CFTR Membrane-Spanning Domains Interface Rescues Some Misfolded Mutants. Int J Mol Sci 2022; 23:ijms232416225. [PMID: 36555865 PMCID: PMC9780841 DOI: 10.3390/ijms232416225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
ABC transporters are large membrane proteins sharing a complex architecture, which comprises two nucleotide-binding domains (NBDs) and two membrane-spanning domains (MSDs). These domains are susceptible to mutations affecting their folding and assembly. In the CFTR (ABCC7) protein, a groove has been highlighted in the MSD1 at the level of the membrane inner leaflet, containing both multiple mutations affecting folding and a binding site for pharmaco-chaperones that stabilize this region. This groove is also present in ABCB proteins, however it is covered by a short elbow helix, while in ABCC proteins it remains unprotected, due to a lower position of the elbow helix in the presence of the ABCC-specific lasso motif. Here, we identified a MSD1 second-site mutation located in the vicinity of the CFTR MSD1 groove that partially rescued the folding defect of cystic fibrosis causing mutations located within MSD1, while having no effect on the most frequent mutation, F508del, located within NBD1. A model of the mutated protein 3D structure suggests additional interaction between MSD1 and MSD2, strengthening the assembly at the level of the MSD intracellular loops. Altogether, these results provide insightful information in understanding key features of the folding and function of the CFTR protein in particular, and more generally, of type IV ABC transporters.
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Affiliation(s)
- Nesrine Baatallah
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Ahmad Elbahnsi
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Benoit Chevalier
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Solène Castanier
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Jean-Paul Mornon
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Iwona Pranke
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Aleksander Edelman
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
- Correspondence: (I.C.); (A.H.)
| | - Alexandre Hinzpeter
- INSERM, U1151, Institut Necker Enfants Malades (INEM), Faculté de Médecine, Université Paris Cité, CNRS, UMR 8253, 75015 Paris, France
- Correspondence: (I.C.); (A.H.)
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137
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Jogini V, Jensen MØ, Shaw DE. Gating and modulation of an inward-rectifier potassium channel. J Gen Physiol 2022; 155:213765. [PMID: 36524993 PMCID: PMC9764021 DOI: 10.1085/jgp.202213085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Inward-rectifier potassium channels (Kirs) are lipid-gated ion channels that differ from other K+ channels in that they allow K+ ions to flow more easily into, rather than out of, the cell. Inward rectification is known to result from endogenous magnesium ions or polyamines (e.g., spermine) binding to Kirs, resulting in a block of outward potassium currents, but questions remain regarding the structural and dynamic basis of the rectification process and lipid-dependent channel activation. Here, we present the results of long-timescale molecular dynamics simulations starting from a crystal structure of phosphatidylinositol 4,5-bisphosphate (PIP2)-bound chicken Kir2.2 with a non-conducting pore. After introducing a mutation (G178R) that is known to increase the open probability of a homologous channel, we were able to observe transitions to a stably open, ion-conducting pore, during which key conformational changes occurred in the main activation gate and the cytoplasmic domain. PIP2 binding appeared to increase stability of the pore in its open and conducting state, as PIP2 removal resulted in pore closure, with a median closure time about half of that with PIP2 present. To investigate structural details of inward rectification, we simulated spermine binding to and unbinding from the open pore conformation at positive and negative voltages, respectively, and identified a spermine-binding site located near a previously hypothesized site between the pore cavity and the selectivity filter. We also studied the effects of long-range electrostatics on conduction and spermine binding by mutating charged residues in the cytoplasmic domain and found that a finely tuned charge density, arising from basic and acidic residues within the cytoplasmic domain, modulated conduction and rectification.
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Affiliation(s)
| | | | - David E. Shaw
- D. E. Shaw Research, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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138
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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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139
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Grüning G, Wong SY, Gerhards L, Schuhmann F, Kattnig DR, Hore PJ, Solov’yov IA. Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes. J Am Chem Soc 2022; 144:22902-22914. [DOI: 10.1021/jacs.2c06233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Gesa Grüning
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Siu Ying Wong
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Fabian Schuhmann
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Daniel R. Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - P. J. Hore
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Ilia A. Solov’yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Institut für Physik, Ammerländer Heerstreet 114-118, 26129 Oldenburg, Germany
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140
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Röhrig UF, Majjigapu SR, Vogel P, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascenção K, Irving M, Coukos G, Michielin O, Zoete V. Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. J Enzyme Inhib Med Chem 2022; 37:1773-1811. [PMID: 35758198 PMCID: PMC9246256 DOI: 10.1080/14756366.2022.2089665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The haem enzyme indoleamine 2,3-dioxygenase 1 (IDO1) catalyses the rate-limiting step in the kynurenine pathway of tryptophan metabolism and plays an essential role in immunity, neuronal function, and ageing. Expression of IDO1 in cancer cells results in the suppression of an immune response, and therefore IDO1 inhibitors have been developed for use in anti-cancer immunotherapy. Here, we report an extension of our previously described highly efficient haem-binding 1,2,3-triazole and 1,2,4-triazole inhibitor series, the best compound having both enzymatic and cellular IC50 values of 34 nM. We provide enzymatic inhibition data for almost 100 new compounds and X-ray diffraction data for one compound in complex with IDO1. Structural and computational studies explain the dramatic drop in activity upon extension to pocket B, which has been observed in diverse haem-binding inhibitor scaffolds. Our data provides important insights for future IDO1 inhibitor design.
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Affiliation(s)
- Ute F Röhrig
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Somi Reddy Majjigapu
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nahzli Dilek
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Kelly Ascenção
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - George Coukos
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Olivier Michielin
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research-Lausanne Branch, Lausanne, CH-1011, Switzerland
| | - Vincent Zoete
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
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141
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Bondar AN. Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184052. [PMID: 36116514 DOI: 10.1016/j.bbamem.2022.184052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 08/17/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Proteins that bind protons at cell membrane interfaces often expose to the bulk clusters of carboxylate and histidine sidechains that capture protons transiently and, in proton transporters, deliver protons to an internal site. The protonation-coupled dynamics of bulk-exposed carboxylate clusters, also known as proton antennas, is poorly described. An essential open question is how water-mediated bridges between sidechains of the cluster respond to protonation change and facilitate transient proton storage. To address this question, here I studied the protonation-coupled dynamics at the proton-binding antenna of PsbO, a small extrinsinc subunit of the photosystem II complex, with atomistic molecular dynamics simulations and systematic graph-based analyses of dynamic protein and protein-water hydrogen-bond networks. The protonation of specific carboxylate groups is found to impact the dynamics of their local protein-water hydrogen-bond clusters. Regardless of the protonation state considered for PsbO, carboxylate pairs that can sample direct hydrogen bonding, or bridge via short hydrogen-bonded water chains, anchor to nearby basic or polar protein sidechains. As a result, carboxylic sidechains of the hypothesized antenna cluster are part of dynamic hydrogen bond networks that may rearrange rapidly when the protonation changes.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, 52425 Jülich, Germany; Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, D-14195 Berlin, Germany.
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142
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Camisasca G, Tenuzzo L, Gallo P. Protein hydration water: focus on low density and high density local structures upon cooling. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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143
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Yamane T, Ekimoto T, Ikeguchi M. Development of the force field for cyclosporine A. Biophys Physicobiol 2022; 19:e190045. [PMID: 36567735 PMCID: PMC9751258 DOI: 10.2142/biophysico.bppb-v19.0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022] Open
Abstract
Membrane permeability of cyclic peptides is an important factor in drug design. To investigate the membrane permeability of cyclic peptides using molecular dynamics (MD) simulations, the accurate force fields for unnatural amino acids present in the cyclic peptides are required. Therefore, we developed the CHARMM force fields of the unnatural amino acids present in cyclosporin A (CsA), a cyclic peptide used as an immune suppressor. Especially for N-methyl amino acids, which contribute to the membrane permeability of cyclic peptides, we developed a grid correction map (CMAP) of the energy surface using the φ and ψ dihedral angles in the main chain of CsA. To validate the developed force field, we performed MD simulations, including the generalized replica exchange with solute tempering method, of CsA in water and chloroform solvents. The conformations of CsA in water and chloroform sampled using the developed force field were consistent with those of the experimental results of the solution nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Tsutomu Yamane
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan,HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan,HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
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144
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Vogel P, Möller N, Qaisrani MN, Bista P, Weber SAL, Butt HJ, Liebchen B, Sulpizi M, Palberg T. Charging of Dielectric Surfaces in Contact with Aqueous Electrolytes─the Influence of CO 2. J Am Chem Soc 2022; 144:21080-21087. [DOI: 10.1021/jacs.2c06793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Peter Vogel
- Institute of Physics, Johannes Gutenberg University, 55128Mainz, Germany
| | - Nadir Möller
- Institute of Physics, Johannes Gutenberg University, 55128Mainz, Germany
| | | | - Pravash Bista
- Max Planck Institute for Polymer Research, 55128Mainz, Germany
| | | | | | - Benno Liebchen
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289Darmstadt, Germany
| | - Marialore Sulpizi
- Department of Physics, Ruhr Universität Bochum, 44780Bochum, Germany
| | - Thomas Palberg
- Institute of Physics, Johannes Gutenberg University, 55128Mainz, Germany
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145
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Wilson MA, Pohorille A. Structure and Computational Electrophysiology of Ac-LS3, a Synthetic Ion Channel. J Phys Chem B 2022; 126:8985-8999. [PMID: 36306164 DOI: 10.1021/acs.jpcb.2c05965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Computer simulations are reported on Ac-LS3, a synthetic ion channel, containing 21 residues with a Leu-Ser-Ser-Leu-Leu-Ser-Leu heptad repeat, which forms ions channels upon application of voltage. A hexameric, coiled-coil bundle initially positioned perpendicular to the membrane settled into a stable, tilted structure after 1.5 μs, most likely to improve contacts between the non-polar exterior of the channel and the hydrophobic core of the membrane. Once tilted, the bundle remained in this state during subsequent simulations of nearly 10 μs at voltages ranging from 200 to -100 mV. In contrast, attempts to identify a stable pentameric structure failed, thus supporting the hypothesis that the channel is a hexamer. Results at 100 mV were used to reconstruct the free energy profiles for K+ and Cl- in the channel. This was done by way of several methods in which results of molecular dynamics (MD) simulations were combined with the electrodiffusion model. Two of them developed recently do not require knowledge of the diffusivity. Instead, they utilize one-sided density profiles and committor probabilities. The consistency between different methods is very good, supporting the utility of the newly developed methods for reconstructing free energies of ions in channels. The flux of K+, which accounts for most of the current through the channel, calculated directly from MD matches well the total measured current. However, the current of Cl- is somewhat overestimated, possibly due to a slightly unbalanced force field involving chloride. The current-voltage dependence was also reconstructed by way of a recently developed, efficient method that requires simulations only at a single voltage, yielding good agreement with the experiment. Taken together, the results demonstrate that computational electrophysiology has become a reliable tool for studying how channels mediate ion transport through membranes.
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Affiliation(s)
- Michael A Wilson
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94035, United States.,SETI Institute, 189 Bernardo Avenue, Suite 200, Mountain View, California94043, United States
| | - Andrew Pohorille
- Exobiology Branch, MS239-4, NASA Ames Research Center, Moffett Field, California94033, United States.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California94132, United States
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146
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Nasou AG, Pantatosaki E, Papadopoulos GK. A Simulation Study of the Effect of Naturally Occurring Point Mutations on the SRY-DNA Complex. J Phys Chem B 2022; 126:8921-8930. [PMID: 36315187 DOI: 10.1021/acs.jpcb.2c04852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular dynamics (MD) simulations were conducted in order to investigate the effect of the naturally occurring point mutations of the transcription factor (TF) sex-determining region Y (SRY) on the structure and dynamics of the SRY-DNA complex. The normal SRY, along with the two mutants I13T and G40R, comprising point mutations on the SRY chain, which have been clinically identified in patients with sex developmental disorders, were modeled as DNA complexes. Our modeling work aims at elucidating atomic-level structural determinants of the aberrant SRY-DNA complexation by means of μs-long MD. The results suggest that the observed disorders brought about by the G40R-DNA and I13T-DNA may arise predominantly from the destabilization of the complex being in accord with in vitro assays found elsewhere and from modifications of the DNA bending as revealed in this study. Comparative potential of mean force computations, over a sequence of short separation distances for the three complexes, verified a higher stability of the normal SRY-DNA. Examining the way the SRY mutations modulate the SRY-DNA complex dynamics at the microscopic level is important also toward elucidating molecular determinants of function for proteins capable of binding to DNA.
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Affiliation(s)
- Angeliki-Georgia Nasou
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
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147
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Yang X, Wu W, Chen X, Wu F, Fan S, Yu P, Mao L. A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution. SCIENCE ADVANCES 2022; 8:eabo3315. [PMID: 36322668 PMCID: PMC9629707 DOI: 10.1126/sciadv.abo3315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Artificial metalloenzymes (ArMs) are commonly designed with protein scaffolds containing buried coordination pockets to achieve substrate specificity and product selectivity for homogeneous reactions. However, their reactivities toward heterogeneous transformations are limited because interfacial electron transfers are hampered by the backbone shells. Here, we introduce bacterial small laccase (SLAC) as a new protein scaffold for constructing ArMs to directly catalyze electrochemical transformations. We use molecular dynamics simulation, x-ray crystallography, spectroscopy, and computation to illustrate the scaffold-directed assembly of an oxo-bridged dicobalt motif on protein surface. The resulting ArM in aqueous phase catalyzes electrochemical water oxidation without mediators or electrode modifications. Mechanistic investigation reveals the role of SLAC scaffold in defining the four-electron transfer pathway from water to oxygen. Furthermore, we demonstrate that SLAC-based ArMs implemented with Ni2+, Mn2+, Ru3+, Pd2+, or Ir3+ also enable direct bioelectrocatalysis of water electrolysis. Our study provides a versatile and generalizable route to complement heterogeneous repertoire of ArMs for expanded applications.
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Affiliation(s)
- Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Fan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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148
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Fuladi S, McGuinness S, Shen L, Weber CR, Khalili-Araghi F. Molecular mechanism of claudin-15 strand flexibility: A computational study. J Gen Physiol 2022; 154:213632. [PMID: 36318156 PMCID: PMC9629798 DOI: 10.1085/jgp.202213116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/30/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Claudins are one of the major components of tight junctions that play a key role in the formation and maintenance of the epithelial barrier function. Tight junction strands are dynamic and capable of adapting their structure in response to large-scale tissue rearrangement and cellular movement. Here, we present molecular dynamics simulations of claudin-15 strands of up to 225 nm in length in two parallel lipid membranes and characterize their mechanical properties. The persistence length of claudin-15 strands is comparable with those obtained from analyses of freeze-fracture electron microscopy. Our results indicate that lateral flexibility of claudin strands is due to an interplay of three sets of interfacial interaction networks between two antiparallel double rows of claudins in the membranes. In this model, claudins are assembled into interlocking tetrameric ion channels along the strand that slide with respect to each other as the strands curve over submicrometer-length scales. These results suggest a novel molecular mechanism underlying claudin-15 strand flexibility. It also sheds light on intermolecular interactions and their role in maintaining epithelial barrier function.
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Affiliation(s)
- Shadi Fuladi
- Department of Physics, University of Illinois, Chicago, IL
| | - Sarah McGuinness
- Department of Bioengineering, University of Illinois, Chicago, IL
| | - Le Shen
- Department of Surgery, The University of Chicago, Chicago, IL
| | | | - Fatemeh Khalili-Araghi
- Department of Physics, University of Illinois, Chicago, IL,Correspondence to Fatemeh Khalili-Araghi:
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Jiang M, Wang B, Ye R, Yu N, Xie Z, Hua Y, Zhou R, Tian B, Dai S. Evidence and Impacts of Nanoplastic Accumulation on Crop Grains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202336. [PMID: 36251925 PMCID: PMC9685458 DOI: 10.1002/advs.202202336] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/22/2022] [Indexed: 05/19/2023]
Abstract
Nanoplastics are emerging pollutants of global concern. Agricultural soil is becoming a primary sink for nanoplastics generated from plastic debris. The uptake and accumulation of nanoplastics by crops contaminate the food chain and pose unexpected risks to human health. However, whether nanoplastics can enter grains and their impact on the grains of crop grown in contaminated soil is still unknown. Here, the translocation of polystyrene nanoplastics (PS-NPs) in crops, including peanut (Arachis hypogaea L.) and rice (Oryza sativa L.) is investigated. It is demonstrated PS-NPs translocation from the root and accumulation in the grains at the maturation stage. The treatment with PS-NPs (250 mg kg-1 ) increases the empty-shell numbers of rice grain by 35.45%, thereby decreasing the seed-setting rate of rice by 3.02%, and also decreases the average seed weight of peanuts by 3.45%. Moreover, PS-NPs exerted adverse effects on nutritional quality, such as decreasing the content of mineral elements, amino acids, and unsaturated fatty acids. To the knowledge, this is the first report of the presence of nanoplastics in the grains of crop plants grown in soil containing nanoplastics, and the results highlight the impact of nanoplastics on the yield and nutritional quality of crop grains.
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Affiliation(s)
- Meng Jiang
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
- Hainan InstituteZhejiang UniversityYazhou Bay Sci‐Tech CitySanya572025P. R. China
- National Key Laboratory of Rice BiologyInstitute of Crop SciencesZhejiang UniversityHangzhou310012P. R. China
| | - Binqiang Wang
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
| | - Rui Ye
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
- School of PhysicsInstitute of Quantitative BiologyZhejiang UniversityHangzhou310012P. R. China
| | - Ning Yu
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
| | - Zhenming Xie
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
- School of PhysicsInstitute of Quantitative BiologyZhejiang UniversityHangzhou310012P. R. China
- Cancer CenterZhejiang UniversityHangzhou310012P. R. China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
- Cancer CenterZhejiang UniversityHangzhou310012P. R. China
| | - Shang Dai
- MOE Key Laboratory of Biosystems Homeostasis & ProtectionCollege of Life SciencesZhejiang UniversityHangzhou310012P. R. China
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150
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Pandey MP, Sasidharan S, Raghunathan VA, Khandelia H. Molecular Mechanism of Hydrotropic Properties of GTP and ATP. J Phys Chem B 2022; 126:8486-8494. [PMID: 36251789 DOI: 10.1021/acs.jpcb.2c06077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hydrotropes are small amphiphilic compounds that increase the aqueous solubility of hydrophobic molecules. Recent evidence suggests that adenosine triphosphate (ATP), which is the primary energy carrier in cells, also assumes hydrotropic properties to prevent the aggregation of hydrophobic proteins, but the mechanism of hydrotropy is unknown. Here, we compare the hydrotropic behavior of all four biological nucleoside triphosphates (NTPs) using molecular dynamics (MD) simulations. We launch all atom MD simulations of aqueous solutions of NTPs [ATP, guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)] with pyrene, which acts both as a model hydrophobic compound and as a spectroscopic reporter for aggregation. GTP prevents pyrene aggregation effectively. Dissolution is not achieved in the presence of CTP and UTP. The higher stability of the base stacking in guanine is responsible for the higher hydrotropic efficiency of GTP. Consistent with the simulations, spectroscopic measurements also suggest that the hydrotropic activity of GTP is higher than ATP. Stacking of aromatic pyrene with the aromatic base of NTPs is a characteristic feature of this hydrotropic property. Both ATP and GTP also dissolve clusters of di- and tripeptides containing tryptophan but with equal potency. Importantly, the presence of aromatic amino acids is a necessary condition for the hydrotropic potency of ATP and GTP. Our results can have broad implications for hydrotrope design in the pharmaceutical industry, as well as the possibility of cells employing GTP as a hydrotrope to regulate the hydrophobic protein aggregation in membrane-less biological condensates.
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Affiliation(s)
- Mayank Prakash Pandey
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
| | | | | | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense5230, Denmark
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