1
|
Sharma B, Koren DT, Ghosh S. Nitric oxide modulates NMDA receptor through a negative feedback mechanism and regulates the dynamical behavior of neuronal postsynaptic components. Biophys Chem 2023; 303:107114. [PMID: 37832215 DOI: 10.1016/j.bpc.2023.107114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023]
Abstract
Nitric oxide (NO) is known to be an important regulator of neurological processes in the central nervous system which acts directly on the presynaptic neuron and enhances the release of neurotransmitters like glutamate into the synaptic cleft. Calcium influx activates a cascade of biochemical reactions to influence the production of nitric oxide in the postsynaptic neuron. This has been modeled in the present work as a system of ordinary differential equations, to explore the dynamics of the interacting components and predict the dynamical behavior of the postsynaptic neuron. It has been hypothesized that nitric oxide modulates the NMDA receptor via a feedback mechanism and regulates the dynamic behavior of postsynaptic components. Results obtained by numerical analyses indicate that the biochemical system is stimulus-dependent and shows oscillations of calcium and other components within a limited range of concentration. Some of the parameters such as stimulus strength, extracellular calcium concentration, and rate of nitric oxide feedback are crucial for the dynamics of the components in the postsynaptic neuron.
Collapse
Affiliation(s)
- Bhanu Sharma
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India
| | | | - Subhendu Ghosh
- Department of Biophysics, University of Delhi South Campus, New Delhi 110021, India.
| |
Collapse
|
2
|
Mazumder M, Kumar S, Kumar D, Bhattacharya A, Gourinath S. Machine learning-based modulation of Ca 2+-binding affinity in EF-hand proteins and comparative structural insights into site-specific cooperative binding. Int J Biol Macromol 2023; 248:125866. [PMID: 37473887 DOI: 10.1016/j.ijbiomac.2023.125866] [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: 01/20/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we report two new scoring schemes enabling the user to estimate and manipulate the calcium binding affinities in EF hand containing proteins. To validate this, we designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues. The N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1) is used for site-directed mutagenesis to incorporate the designed loop sequence into the second EF-hand motif of this protein, referred as Nt-EhCaBP1-EF2 mutant. The binding isotherms calculated using ITC calorimetry showed that Nt-EhCaBP1-EF2 mutant site binds Ca2+ with higher affinity than Wt-Nt-EhCaBP1, by ∼600 times. The crystal structure of the mutant displayed more compact Ca2+-coordination spheres in both of its EF loops than the structure of the wildtype protein. The compact coordination sphere of EF-2 causes the bend in the helix-3, which leads to the formation of unexpected hexamer of NtEhCaBP1-EF2 mutant structure. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in stronger coordination of Ca2+ even in another EF-hand loop.
Collapse
Affiliation(s)
- Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Pine Biotech, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Sanjeev Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, Nashville, TN 37232-0146, USA
| | - Devbrat Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - S Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| |
Collapse
|
3
|
Orr AA, Tao A, Guvench O, MacKerell AD. Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction. Mol Pharm 2023; 20:2600-2611. [PMID: 37017675 PMCID: PMC10159941 DOI: 10.1021/acs.molpharmaceut.3c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Protein-based therapeutics typically require high concentrations of the active protein, which can lead to protein aggregation and high solution viscosity. Such solution behaviors can limit the stability, bioavailability, and manufacturability of protein-based therapeutics and are directly influenced by the charge of a protein. Protein charge is a system property affected by its environment, including the buffer composition, pH, and temperature. Thus, the charge calculated by summing the charges of each residue in a protein, as is commonly done in computational methods, may significantly differ from the effective charge of the protein as these calculations do not account for contributions from bound ions. Here, we present an extension of the structure-based approach termed site identification by ligand competitive saturation-biologics (SILCS-Biologics) to predict the effective charge of proteins. The SILCS-Biologics approach was applied on a range of protein targets in different salt environments for which membrane-confined electrophoresis-determined charges were previously reported. SILCS-Biologics maps the 3D distribution and predicted occupancy of ions, buffer molecules, and excipient molecules bound to the protein surface in a given salt environment. Using this information, the effective charge of the protein is predicted such that the concentrations of the ions and the presence of excipients or buffers are accounted for. Additionally, SILCS-Biologics also produces 3D structures of the binding sites of ions on the proteins, which enable further analyses such as the characterization of protein surface charge distribution and dipole moments in different environments. Notable is the capability of the method to account for competition between salts, excipients, and buffers on the calculated electrostatic properties in different protein formulations. Our study demonstrates the ability of the SILCS-Biologics approach to predict the effective charge of proteins and its applicability in uncovering protein-ion interactions and their contributions to protein solubility and function.
Collapse
Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| | - Aoxiang Tao
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Olgun Guvench
- SilcsBio LLC, 1100 Wicomico Street, Suite 323, Baltimore, MD, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, MD, USA
| |
Collapse
|
4
|
Cen X, Liu B, Zhang G, Liu H, Yao G, He M, Liu W. Molecular identification of a novel antimicrobial peptide in giant Triton snail Charonia tritonis: mRNA profiles for tissues and its potential antibacterial activity. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108734. [PMID: 37028689 DOI: 10.1016/j.fsi.2023.108734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Antimicrobial peptides (AMPs) play an important role in innate immunity against microorganisms. AMPs is an effective antibacterial agent, and the chances of causing pathogens to develop is very low. However, there is little information about AMPs in the giant Triton snail Charonia tritonis. In this research, an antimicrobial peptide gene (termed Ct-20534) was identified in C. tritonis. The open reading frame of Ct-20534 is 381 bp in size and it encodes a basic peptide precursor containing 126 amino acids. Ct-20534 gene was found to be expressed in all five tissues examined by real-time fluorescence quantitative PCR (qPCR), but the highest expression was found in the proboscis. This is the first report that antibacterial peptides have been found in C. tritonis, and it has been proved that Ct-20534 has antibacterial activity against Gram-positive bacteria and Gram-negative bacteria, among which the activity of Staphylococcus aureus is most significantly inhibited, this suggests that the newly discovered antimicrobial peptides in C. tritonis may play an important role in the immune system and bacterial resistance of C. tritonis. This study presents the discovery of a newly identified antibacterial peptide from C. tritonis, with its structural properties fully characterized and potent antibacterial activity confirmed. The results provide essential fundamental data for the development of preventive and therapeutic measures against aquatic animal diseases, which in turn can promote the sustainable and stable growth of the aquaculture industry and create economic benefits. Additionally, this research lays the foundation for future development of novel anti-infective drugs.
Collapse
Affiliation(s)
- Xitong Cen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gege Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiru Liu
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Department of Fishery Sciences, Tianjin Agricultural University, Tianjin, 300384, China
| | - Gaoyou Yao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, China
| | - Wenguang Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, China.
| |
Collapse
|
5
|
Nde J, Zhang P, Waxham MN, Cheung MS. Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin's Calcium-Binding Properties. J Phys Chem B 2023; 127:2900-2908. [PMID: 36977372 DOI: 10.1021/acs.jpcb.2c08734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
We aim to elucidate the molecular mechanism of the reciprocal relation of calmodulin's (CaM) target binding and its affinity for calcium ions (Ca2+), which is central to decoding CaM-dependent Ca2+ signaling in a cell. We employed stopped-flow experiments and coarse-grained molecular simulations that learn the coordination chemistry of Ca2+ in CaM from first-principle calculations. The associative memories as part of the coarse-grained force fields built on known protein structures further influence CaM's selection of its polymorphic target peptides in the simulations. We modeled the peptides from the Ca2+/CaM-binding domain of Ca2+/CaM-dependent kinase II (CaMKII), CaMKIIp (293-310) and selected distinctive mutations at the N-terminus. Our stopped-flow experiments have shown that the CaM's affinity for Ca2+ in the bound complex of Ca2+/CaM/CaMKIIp decreased significantly when Ca2+/CaM bound to the mutant peptide (296-AAA-298) compared to that bound to the wild-type peptide (296-RRK-298). The coarse-grained molecular simulations revealed that the 296-AAA-298 mutant peptide destabilized the structures of Ca2+-binding loops at the C-domain of CaM (c-CaM) due to both loss of electrostatic interactions and differences in polymorphic structures. We have leveraged a powerful coarse-grained approach to advance a residue-level understanding of the reciprocal relation in CaM, that could not be possibly achieved by other computational approaches.
Collapse
Affiliation(s)
- Jules Nde
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
| | - Pengzhi Zhang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Margaret S Cheung
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| |
Collapse
|
6
|
Liu X, Zheng L, Qin C, Zhang JZH, Sun Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. J Comput Aided Mol Des 2022; 36:735-752. [PMID: 36136209 DOI: 10.1007/s10822-022-00475-0] [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: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Despite the massive application of end-point free energy methods in protein-ligand and protein-protein interactions, computational understandings about their performance in relatively simple and prototypical host-guest systems are limited. In this work, we present a comprehensive benchmark calculation with standard end-point free energy techniques in a recent host-guest dataset containing 13 host-guest pairs involving the carboxylated-pillar[6]arene host. We first assess the charge schemes for solutes by comparing the charge-produced electrostatics with many ab initio references, in order to obtain a preliminary albeit detailed view of the charge quality. Then, we focus on four modelling details of end-point free energy calculations, including the docking procedure for the generation of initial condition, the charge scheme for host and guest molecules, the water model used in explicit-solvent sampling, and the end-point methods for free energy estimation. The binding thermodynamics obtained with different modelling schemes are compared with experimental references, and some practical guidelines on maximizing the performance of end-point methods in practical host-guest systems are summarized. Further, we compare our simulation outcome with predictions in the grand challenge and discuss further developments to improve the prediction quality of end-point free energy methods. Overall, unlike the widely acknowledged applicability in protein-ligand binding, the standard end-point calculations cannot produce useful outcomes in host-guest binding and thus are not recommended unless alterations are performed.
Collapse
Affiliation(s)
- Xiao Liu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China.
| | - Lei Zheng
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Chu Qin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.,Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Zhaoxi Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| |
Collapse
|