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Wang Q, DiForte C, Aleshintsev A, Elci G, Bhattacharya S, Bongiorno A, Gupta R. Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins. Protein Sci 2024; 33:e4955. [PMID: 38501487 PMCID: PMC10949321 DOI: 10.1002/pro.4955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024]
Abstract
Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein. Elimination of binding in S100-specific EF-I loop has limited impact on the calcium binding affinity of the EF-II loop and the concomitant structural rearrangement. In contrast, deletion of binding in the EF-II loop significantly attenuates calcium affinity in the EF-I loop and the structure adopts a 'closed' apo-like conformation. Analysis of experimental amide nitrogen (15 N) relaxation rates (R1 , R2 , and 15 N-{1 H} NOE) and molecular dynamics (MD) simulations demonstrate that the calcium bound state is relatively floppy with pico-nanosecond motions induced in functionally relevant domains responsible for target recognition such as the hinge domain and the C-terminal residues. Experimental relaxation studies combined with MD simulations show that while calcium binding in the EF-I loop alone does not induce significant motions in the polypeptide chain, EF-I regulates fluctuations in the polypeptide in the presence of bound calcium in the EF-II loop. These results offer novel insights into the dynamic regulation of target recognition by calcium binding and unravels the role of cooperativity between the two calcium binding events in S100A12.
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Affiliation(s)
- Qian Wang
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | - Christopher DiForte
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Aleksey Aleshintsev
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Gianna Elci
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
| | | | - Angelo Bongiorno
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
| | - Rupal Gupta
- Department of ChemistryCollege of Staten Island, City University of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry and ChemistryThe Graduate Center of the City University of New YorkUnited States
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Yoder MW, Wright NT, Borzok MA. Calpain Regulation and Dysregulation-Its Effects on the Intercalated Disk. Int J Mol Sci 2023; 24:11726. [PMID: 37511485 PMCID: PMC10380737 DOI: 10.3390/ijms241411726] [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: 06/30/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The intercalated disk is a cardiac specific structure composed of three main protein complexes-adherens junctions, desmosomes, and gap junctions-that work in concert to provide mechanical stability and electrical synchronization to the heart. Each substructure is regulated through a variety of mechanisms including proteolysis. Calpain proteases, a class of cysteine proteases dependent on calcium for activation, have recently emerged as important regulators of individual intercalated disk components. In this review, we will examine how calcium homeostasis regulates normal calpain function. We will also explore how calpains modulate gap junctions, desmosomes, and adherens junctions activity by targeting specific proteins, and describe the molecular mechanisms of how calpain dysregulation leads to structural and signaling defects within the heart. We will then examine how changes in calpain activity affects cardiomyocytes, and how such changes underlie various heart diseases.
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Affiliation(s)
- Micah W Yoder
- Biochemistry, Chemistry, Engineering, and Physics Department, Commonwealth University of Pennsylvania, 31 Academy St., Mansfield, PA 16933, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, USA
| | - Maegen A Borzok
- Biochemistry, Chemistry, Engineering, and Physics Department, Commonwealth University of Pennsylvania, 31 Academy St., Mansfield, PA 16933, USA
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Basit A, Yadav AK, Bandyopadhyay P. Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. J Chem Inf Model 2022; 62:2821-2834. [PMID: 35608259 DOI: 10.1021/acs.jcim.2c00428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of calcium ions (Ca2+) to the calcium-binding proteins (CBPs) controls a plethora of regulatory processes. Among the roles played by CBPs in several diseases, the onset and progress of some cardiovascular diseases are caused by mutations in calmodulin (CaM), an important member of CBPs. Rationalization and prediction of the binding affinity of Ca2+ ions to the CaM can play important roles in understanding the origin of cardiovascular diseases. However, there is no robust structure-based computational method for predicting the binding affinity of Ca2+ ions to the different forms of CBPs in general and CaM in particular. In the current work, we have devised a fast yet accurate computational technique to accurately calculate the binding affinity of Ca2+ to the different forms of CaM. This method combines the well-known molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method and a charge scaling approach developed by previous authors that takes care of the polarization of CaM and Ca2+ ions. Our detailed analysis of the different components of binding free energy shows that subtle changes in electrostatics and van der Waals contribute to the difference in the binding affinity of mutants from that of the wild type (WT), and the charge scaling approach is superior in calculating these subtle changes in electrostatics as compared to the nonpolarizable force field used in this work. A statistically significant regression model made from our binding free energy calculations gives a correlation coefficient close to 0.8 to the experimental results. This structure-based predictive model can open up a new strategy to understand and predict the binding of Ca2+ to the mutants of CBPs, in general.
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Affiliation(s)
- Abdul Basit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ajeet Kumar Yadav
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Godoy LD, Prizon T, Rossignoli MT, Leite JP, Liberato JL. Parvalbumin Role in Epilepsy and Psychiatric Comorbidities: From Mechanism to Intervention. Front Integr Neurosci 2022; 16:765324. [PMID: 35250498 PMCID: PMC8891758 DOI: 10.3389/fnint.2022.765324] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
Parvalbumin is a calcium-binding protein present in inhibitory interneurons that play an essential role in regulating many physiological processes, such as intracellular signaling and synaptic transmission. Changes in parvalbumin expression are deeply related to epilepsy, which is considered one of the most disabling neuropathologies. Epilepsy is a complex multi-factor group of disorders characterized by periods of hypersynchronous activity and hyperexcitability within brain networks. In this scenario, inhibitory neurotransmission dysfunction in modulating excitatory transmission related to the loss of subsets of parvalbumin-expressing inhibitory interneuron may have a prominent role in disrupted excitability. Some studies also reported that parvalbumin-positive interneurons altered function might contribute to psychiatric comorbidities associated with epilepsy, such as depression, anxiety, and psychosis. Understanding the epileptogenic process and comorbidities associated with epilepsy have significantly advanced through preclinical and clinical investigation. In this review, evidence from parvalbumin altered function in epilepsy and associated psychiatric comorbidities were explored with a translational perspective. Some advances in potential therapeutic interventions are highlighted, from current antiepileptic and neuroprotective drugs to cutting edge modulation of parvalbumin subpopulations using optogenetics, designer receptors exclusively activated by designer drugs (DREADD) techniques, transcranial magnetic stimulation, genome engineering, and cell grafting. Creating new perspectives on mechanisms and therapeutic strategies is valuable for understanding the pathophysiology of epilepsy and its psychiatric comorbidities and improving efficiency in clinical intervention.
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Affiliation(s)
- Lívea Dornela Godoy
- Department of Psychology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Tamiris Prizon
- Department of Neuroscience and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Matheus Teixeira Rossignoli
- Department of Neuroscience and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - João Pereira Leite
- Department of Neuroscience and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- João Pereira Leite,
| | - José Luiz Liberato
- Department of Neuroscience and Behavioral Sciences, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- *Correspondence: José Luiz Liberato,
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Immadisetty K, Polasa A, Shelton R, Moradi M. Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channel. Comput Struct Biotechnol J 2022; 20:2539-2550. [PMID: 35685356 PMCID: PMC9156883 DOI: 10.1016/j.csbj.2022.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
Mechanosensitive channel of large conductance (MscL) detects and responds to changes in the pressure profile of cellular membranes and transduces the mechanical energy into electrical and/or chemical signals. MscL can be activated using ultrasonic or chemical activation methods to improve the absorption of medicines and bioactive compounds into cells. However, re-engineering chemical signals such as pH change can trigger channel activation in MscL. This study elucidates the activation mechanism of an engineered MscL at an atomic level through a combination of equilibrium and non-equilibrium (NE) molecular dynamics (MD) simulations. Comparing the wild-type (WT) and engineered MscL activation processes suggests that the two systems are likely associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various backbone-backbone hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are between the transmembrane helices 1 and 2 in engineered MscL channel. The orientation-based biasing approach for producing and optimizing an open MscL model used in this work is a promising way to characterize unknown protein functional states and investigate the activation processes in ion channels and transmembrane proteins in general. This work paves the way for a computational framework for engineering more efficient pH-sensing mechanosensitive channels.
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Affiliation(s)
- Kalyan Immadisetty
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Reid Shelton
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
- Corresponding author.
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Sun B, Fang X, Johnson C, Hauck G, Kou Y, Davis JP, Kekenes-Huskey PM. Non-Canonical Interaction between Calmodulin and Calcineurin Contributes to the Differential Regulation of Plant-Derived Calmodulins on Calcineurin. J Chem Inf Model 2021; 61:5223-5233. [PMID: 34615359 PMCID: PMC8867402 DOI: 10.1021/acs.jcim.1c00873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Calmodulin (CaM) serves as an important Ca2+ signaling hub that regulates many protein signaling pathways. Recently, it was demonstrated that plant CaM homologues can regulate mammalian targets, often in a manner that opposes the impact of the mammalian CaM (mCaM). However, the molecular basis of how CaM homologue mutations differentially impact target activation is unclear. To understand these mechanisms, we examined two CaM isoforms found in soybean plants that differentially regulate a mammalian target, calcineurin (CaN). These CaM isoforms, sCaM-1 and sCaM-4, share >90 and ∼78% identity with the mCaM, respectively, and activate CaN with comparable or reduced activity relative to mCaM. We used molecular dynamics (MD) simulations and fluorometric assays of CaN-dependent dephosphorylation of MUF-P to probe whether calcium and protein-protein binding interactions are altered by plant CaMs relative to mCaM as a basis for differential CaN regulation. In the presence of CaN, we found that the two sCaMs' Ca2+ binding properties, such as their predicted coordination of Ca2+ and experimentally measured EC50 [Ca2+] values are comparable to mCaM. Furthermore, the binding of CaM to the CaM binding region (CaMBR) in CaN is comparable among the three CaMs, as evidenced by MD-predicted binding energies and experimentally measured EC50 [CaM] values. However, mCaM and sCaM-1 exhibited binding with a secondary region of CaN's regulatory domain that is weakened for sCaM-4. We speculate that this secondary interaction affects the turnover rate (kcat) of CaN based on our modeling of enzyme activity, which is consistent with our experimental data. Together, our data describe how plant-derived CaM variants alter CaN activity through enlisting interactions other than those directly influencing Ca2+ binding and canonical CaMBR binding, which may additionally play a role in the differential regulation of other mammalian targets.
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Affiliation(s)
- Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
| | - Christopher Johnson
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
- Department of Chemistry, Mississippi State University Starkville MS, 39759
| | - Garrett Hauck
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Yongjun Kou
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Jonathan P. Davis
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Peter M. Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, USA 60153
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Immadisetty K, Moradi M. Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus. J Phys Chem B 2021; 125:9738-9750. [PMID: 34424716 DOI: 10.1021/acs.jpcb.1c03982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proton-coupled oligopeptide transporters (POTs) use the proton electrochemical gradient to transport peptides across the cell membrane. Despite the significant biological and biomedical relevance of these proteins, a detailed mechanistic picture for chemomechanical couplings involved in substrate/proton transport and protein structural changes is missing. Therefore, we performed microsecond-level molecular dynamics simulations of bacterial POT PepTSt, which shares ∼80% sequence identity with the human POT, PepT1, in the substrate-binding region. Three different conformational states of PepTSt were simulated, including (i) occluded, apo, (ii) inward-facing, apo, and (iii) inward-facingoccluded, Leu-Ala bound. We propose that the interaction of R33 with E299 and E300 acts as a conformational switch (i.e., to trigger the conformational change from an inward- to outward-facing state) in the substrate transport. Additionally, we propose that E299 and E400 disengage from interacting with the substrate either through protonation or through coordination with a cation for the substrate to get transported. This study provides clues to understand the chemomechanical couplings in POTs and paves the way to decipher the molecular-level underpinnings of the structure-function relationship in this important family of transporters.
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Affiliation(s)
| | - Mahmoud Moradi
- University of Arkansas, Fayetteville, Arkansas 72701, United States
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