1
|
Cholasseri R, De S. Deciphering the shape selective conformational equilibrium of E- and Z-locked azobenzene-tetraethylammonium ion in regulating photo-switchable K +-ion channel blocking. Phys Chem Chem Phys 2024; 26:19161-19175. [PMID: 38973424 DOI: 10.1039/d4cp01604a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
The search for photo-switchable optopharmacological agents that can block ion channels has been a prevalent area owing to its prime advantages of reversibility and specificity over the traditional blockers. However, the quest for a higher blocking ability shown by a less stable photo-isomer to perfectly suit the requirement of the optopharmacological agents is still ongoing. To date, only a marginal improvement in terms of blocking ability is observed by the less stable E-isomer of para-substituted locked azobenzene with TEA (LAB-TEA) for the K+-ion channel. Thus, rationalization of the limitation for achieving high activity by the E-isomer is rather essential to aid the improvement of the efficiency of photoswitchable blocker drugs. Herein, we report a molecular-level analysis on the mechanism of blocking by E- and Z-LAB-TEA with the bacterial KcsA K+-ion channel using Molecular Dynamics (MD) simulation and Quantum Mechanical (QM) calculations. The positively charged TEA fragment engages in stronger electrostatic interactions, while the neutral LAB fragment engages in weaker dispersive interactions. The binding free energy calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) for E-LAB-TEA (-22.3 kcal mol-1) shows less thermodynamic preference for binding with K+-ion channels than Z-LAB-TEA (-21.6 kcal mol-1) corroborating the experimental observation. The correlation between the structure and the binding ability of E- and Z-isomers of LAB-TEA indicates that the channel gate is narrow and acts as a bottleneck for the entry of the binder molecule inside the large cavity. Upon irradiation, the Z-isomer converts into a less stable but long and planar E-isomer (ΔE of photoisomerism = 7.0 kcal mol-1, at SA2-CASPT2(6,4)/6-31+G(d)//CASSCF(6,4)/6-31+G(d)), which is structurally more suitable to fit into the narrow channel gate rather than the curved and non-planar Z-LAB-TEA. Thus, a reduction in the ionic current is observed owing to the preferential entry and subsequent blocking by E-LAB-TEA. Discontinuing the irradiation leads to conversion to the Z-isomer, the curved nature of which hinders its spontaneous release outside the cavity, thereby contributing only a small increase in the ionic current.
Collapse
Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala, 673 601, India
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut University P. O, Malappuram, Kerala, 673 635, India.
| |
Collapse
|
2
|
Sabu G, De S. Be 2+ Causes Hypersensitivity but Mg 2+ and Ca 2+ Do Not─Favorable Metal Coordination Is the Key for Differential Allosteric Modulation and Binding Affinities. J Phys Chem B 2023; 127:10326-10337. [PMID: 38010277 DOI: 10.1021/acs.jpcb.3c05461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the Be2+ ion against its heavier congeners, Mg2+ and Ca2+, by the human leukocyte antigen immunoprotein (HLA-DP2), leading to immunotoxicity. Integrating with our previous mechanistic study on Be2+ toxicity, herein, we have explored the basis of characteristic nontoxicity of Mg2+ and Ca2+ ions despite their in vivo abundance. The ion binding cleft of the HLA-DP2-peptide complex is composed of four acidic residues, p4D and p7E from the peptide and β26E and β69E from the protein. While the tetrahedral coordination site of the smaller Be2+ ion is located deep inside the cavity, hexa- to octa-coordination sites of Mg2+ and Ca2+ ions are located closer to the protein surface. The intrinsic high coordination number of Mg2+/Ca2+ ions induces allosteric modifications on the HLA-DP2_M2 surface, which are atypical for TCR recognition. Furthermore, the lower binding energy of larger Mg2+ and Ca2+ ions with the cavity residues can be correlated to the lower charge density and reduced covalent bonding nature as compared to those of the smaller Be2+ ion. In short, weak binding of Mg2+ and Ca2+ ions and the unfavorable allosteric surface modifications are probably the major determinants for the absence of Mg2+/Ca2+ ion-mediated hypersensitivity in humans.
Collapse
Affiliation(s)
- Gopika Sabu
- Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi 682 022, India
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut University P.O., Malappuram 673 635, Kerala, India
| |
Collapse
|
3
|
The Construction and Analysis of a ceRNA Network Related to Salt-Sensitivity Hypertensives. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8258351. [PMID: 36277897 PMCID: PMC9586768 DOI: 10.1155/2022/8258351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022]
Abstract
Background Salt-sensitivity hypertensives (SSH) are an independent risk factor for cardiovascular disease. However, the mechanism of SSH is not clear. This study is aimed at constructing a competing endogenous RNA (ceRNA) network related to SSH. Methods Data sets were collected from the Gene Expression Omnibus database (GEO) to extract data on salt sensitivity RNA of patients with or without hypertensives in GSE135111. Firstly, we analyzed differentially expressed genes (DEGs, log2FC ≥ 0.5 and P < 0.05) and differentially expressed lncRNAs (DELs, log2FC ≥1 and P<0.05) between SSH and salt-sensitive normotension (SSN). Then, the gene ontology (GO), KEGG pathway enrichment analysis, and PPI network construction of DEGs were performed, and the hub genes in the PPI network by cytoHubba (12 methods) were screened out. Finally, a ceRNA network was constructed based on lncRNA-miRNA-mRNA pairs and hub genes. Results 163 DEGs and 65 DELs were screened out. The GO and KEGG pathway analyses of DEGs were mainly enriched in metabolism (e.g., insulin secretion and cellular response to glucagon stimulus and peptidyl-tyrosine dephosphorylation,) and plasma membrane signaling (e.g., cell adhesion and chemical synaptic transmission and integral component of membrane). Additionally, a ceRNA network, including 1 mRNA (EGLN3), 2 miRNAs (hsa-miR-17-5p and hsa-miR-20b-5p), and 1 lncRNA (C1orf143) was successfully constructed. Conclusions In conclusion, the proposed ceRNA network may help elucidate the regulatory mechanism by which lncRNAs function as ceRNAs and contribute to the pathogenesis of SSH. Importantly, candidate lncRNAs, miRNAs, and mRNAs can be further evaluated as a potential therapeutic targets for SSH.
Collapse
|
4
|
Paul A, Singh S. Identification of a novel calcium activated potassium channel from Leishmania donovani and in silico predictions of its antigenic features. Acta Trop 2021; 220:105922. [PMID: 33878308 DOI: 10.1016/j.actatropica.2021.105922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/08/2021] [Accepted: 04/08/2021] [Indexed: 11/18/2022]
Abstract
Visceral Leishmaniasis is a major neglected tropical disease with increasing incidences of drug resistance. This has led to the search for a suitable drug target for chemotherapeutic intervention. Potassium channels are a family of membrane proteins which play a vital role in homeostasis and any perturbation in them alters cell survival which makes them an attractive target. To characterize a calcium-activated potassium channel from Leishmania donovani (LdKCa), a putative ion-channel like protein which showed sequence similarity with other Trypanosoma cruzi putative potassium channels was selected. It was cloned and expressed with a histidine tag. MALDI confirmed that it is a potassium channel. Homology model of LdKCa was generated by I-TASSER. It is a transmembrane protein localized in the plasma membrane as predicted by DeepLoc tool. In silico analyses of the protein showed that it is a small conductance calcium activated potassium channel. Point mutation in conserved signature domain 'TXGYGD' affects the protein function as predicted by heat map analysis. The LdKCa model predicted amino acids S207, T208 and M236 as ligand-binding sites. The sequence HSLRGRSARVIQLAWRLRKARKVGPHAPSLKQKVYTLVLSWLLT was the highest scoring B-cell epitope. The highest scoring T-cell epitope was RLYSVIVYL. This study may provide new insights into antigenicity features of leishmanial calcium-activated potassium channels.
Collapse
Affiliation(s)
- Anindita Paul
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062, Punjab, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, SAS Nagar, Mohali, 160062, Punjab, India.
| |
Collapse
|
5
|
Barabash M, Gibby WAT, Guardiani C, Luchinsky DG, Luan B, Smolyanitsky A, McClintock PVE. Field-Dependent Dehydration and Optimal Ionic Escape Paths for C 2N Membranes. J Phys Chem B 2021; 125:7044-7059. [PMID: 34115497 PMCID: PMC8279548 DOI: 10.1021/acs.jpcb.1c03255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/29/2021] [Indexed: 11/28/2022]
Abstract
Most analytic theories describing electrostatically driven ion transport through water-filled nanopores assume that the corresponding permeation barriers are bias-independent. While this assumption may hold for sufficiently wide pores under infinitely small bias, transport through subnanometer pores under finite bias is difficult to interpret analytically. Given recent advances in subnanometer pore fabrication and the rapid progress in detailed computer simulations, it is important to identify and understand the specific field-induced phenomena arising during ion transport. Here we consider an atomistic model of electrostatically driven ion permeation through subnanoporous C2N membranes. We analyze probability distributions of ionic escape trajectories and show that the optimal escape path switches between two different configurations depending on the bias magnitude. We identify two distinct mechanisms contributing to field-induced changes in transport-opposing barriers: a weak one arising from field-induced ion dehydration and a strong one due to the field-induced asymmetry of the hydration shells. The simulated current-voltage characteristics are compared with the solution of the 1D Nernst-Planck model. Finally, we show that the deviation of simulated currents from analytic estimates for large fields is consistent with the field-induced barriers and the observed changes in the optimal ion escape path.
Collapse
Affiliation(s)
| | - William A. T. Gibby
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - Carlo Guardiani
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Department
of Mechanical and Aerospace Engineering, Sapienza University, 00184 Rome, Italy
| | - Dmitry G. Luchinsky
- Department
of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Ames
Research Center, KBR, Inc., Moffett Field, California 94035, United States
| | - Binquan Luan
- Computational
Biological Center, IBM Thomas J. Watson
Research, Yorktown
Heights, New York 10598, United States
| | - Alex Smolyanitsky
- Applied
Chemicals and Materials Division, National
Institute of Standards and Technology, Boulder, Colorado 80305, United States
| | | |
Collapse
|
6
|
Gibby WAT, Barabash ML, Guardiani C, Luchinsky DG, McClintock PVE. Physics of Selective Conduction and Point Mutation in Biological Ion Channels. PHYSICAL REVIEW LETTERS 2021; 126:218102. [PMID: 34114848 DOI: 10.1103/physrevlett.126.218102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
We introduce a statistical and linear response theory of selective conduction in biological ion channels with multiple binding sites and possible point mutation. We derive an effective grand-canonical ensemble and generalized Einstein relations for the selectivity filter, assuming strongly coordinated ionic motion, and allowing for ionic Coulomb blockade. The theory agrees well with data from the KcsA K^{+} channel and a mutant. We show that the Eisenman relations for thermodynamic selectivity follow from the condition for fast conduction and find that maximum conduction requires the binding sites to be nearly identical.
Collapse
Affiliation(s)
- W A T Gibby
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - M L Barabash
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| | - C Guardiani
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- Department of Mechanical and Aerospace Engineering, Sapienza University, Rome 00184, Italy
| | - D G Luchinsky
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
- KBR Inc., Ames Research Center, Moffett Field, Mountain View, California 94035, USA
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, United Kingdom
| |
Collapse
|
7
|
Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
Collapse
Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
| |
Collapse
|
8
|
Kanwa N, De SK, Maity A, Chakraborty A. Interaction of aliphatic amino acids with zwitterionic and charged lipid membranes: hydration and dehydration phenomena. Phys Chem Chem Phys 2020; 22:3234-3244. [DOI: 10.1039/c9cp06188f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aliphatic amino acids interact differently in order to induce gelation or fluidization in zwitterionic and charged lipid membranes as a result of hydration or dehydration of the membrane surface.
Collapse
Affiliation(s)
- Nishu Kanwa
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore
- India
| | - Soumya Kanti De
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore
- India
| | - Avijit Maity
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore
- India
| | - Anjan Chakraborty
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore
- India
| |
Collapse
|