1
|
Fang X, Bogdanov V, Davis JP, Kekenes-Huskey PM. Molecular Insights into the MLCK Activation by CaM. J Chem Inf Model 2023; 63:7487-7498. [PMID: 38016288 PMCID: PMC11070109 DOI: 10.1021/acs.jcim.3c00954] [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] [Indexed: 11/30/2023]
Abstract
Calmodulin (CaM) is a universal regulatory protein that modulates numerous cellular processes by using calcium (Ca2+) as the signal. In smooth muscle cells (SMC), one major target of CaM is myosin light chain kinase (MLCK), a kinase that phosphorylates the myosin regulatory light chain and thereby regulates cell contraction. In the absence of CaM, MLCK remains inhibited by its autoinhibitory domain (AID). While it is well established that CaM activates MLCK, the molecular interactions between these two proteins remain elusive due to the lack of structural data. In this work, we constructed a molecular model of mammalian CaM (mCaM) in complex with MLCK leveraging AlphaFold, published biochemical data, and protein-protein docking. The model, along with a strategic set of CaM mutants including a inhibitory variant soybean CaM isoform 4 (sCaM-4), was subject to molecular dynamics (MD) simulations. Using principal component analysis (PCA), we mapped out the transition path for the removal of the AID from the MLCK kinase domain to provide molecular basis of MLCK activation. Additionally, we established MLCK conformations that correspond to the active and inactive states of the kinase. We showed that mCaM and sCaM-4 cause MLCK to undergo the transition to the active and inactive states, respectively. Using two structural metrics, we computed the probabilities of MLCK activation by different CaM variants, which were in good agreement with the experimental data. Distributions along these metrics revealed that different inhibitory CaM variants impair MLCK activation through unique mechanisms. We finally identified molecular contacts that contribute to the MLCK activation by CaM. Overall, we report a de novo molecular model of CaM-MLCK that provides insights into the molecular mechanism of MLCK activation by CaM. The mechanism requires effective removal of the AID while preserving an active configuration of the kinase domain. This mechanism may be shared by other MLCK isoforms and potentially other structurally similar kinases with CaM-mediated regulatory domains.
Collapse
Affiliation(s)
- Xuan Fang
- Department of Cell and Molecular Physiology, Stritch School of medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
| | - Vladimir Bogdanov
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Stritch School of medicine, Loyola University Chicago, Maywood, Illinois 60153, United States
| |
Collapse
|
2
|
Rodriguez Garcia M, Schmeckpeper J, Landim-Vieira M, Coscarella IL, Fang X, Ma W, Spran PA, Yuan S, Qi L, Kahmini AR, Shoemaker MB, Atkinson JB, Kekenes-Huskey PM, Irving TC, Chase PB, Knollmann BC, Pinto JR. Disruption of Z-Disc Function Promotes Mechanical Dysfunction in Human Myocardium: Evidence for a Dual Myofilament Modulatory Role by Alpha-Actinin 2. Int J Mol Sci 2023; 24:14572. [PMID: 37834023 PMCID: PMC10572656 DOI: 10.3390/ijms241914572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The ACTN2 gene encodes α-actinin 2, located in the Z-disc of the sarcomeres in striated muscle. In this study, we sought to investigate the effects of an ACTN2 missense variant of unknown significance (p.A868T) on cardiac muscle structure and function. Left ventricular free wall samples were obtained at the time of cardiac transplantation from a heart failure patient with the ACTN2 A868T heterozygous variant. This variant is in the EF 3-4 domain known to interact with titin and α-actinin. At the ultrastructural level, ACTN2 A868T cardiac samples presented small structural changes in cardiomyocytes when compared to healthy donor samples. However, contractile mechanics of permeabilized ACTN2 A868T variant cardiac tissue displayed higher myofilament Ca2+ sensitivity of isometric force, reduced sinusoidal stiffness, and faster rates of tension redevelopment at all Ca2+ levels. Small-angle X-ray diffraction indicated increased separation between thick and thin filaments, possibly contributing to changes in muscle kinetics. Molecular dynamics simulations indicated that while the mutation does not significantly impact the structure of α-actinin on its own, it likely alters the conformation associated with titin binding. Our results can be explained by two Z-disc mediated communication pathways: one pathway that involves α-actinin's interaction with actin, affecting thin filament regulation, and the other pathway that involves α-actinin's interaction with titin, affecting thick filament activation. This work establishes the role of α-actinin 2 in modulating cross-bridge kinetics and force development in the human myocardium as well as how it can be involved in the development of cardiac disease.
Collapse
Affiliation(s)
| | - Jeffrey Schmeckpeper
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | - Xuan Fang
- Department of Cell & Molecular Physiology, Loyola University, Chicago, IL 60660, USA
| | - Weikang Ma
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Payton A. Spran
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Shengyao Yuan
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Lin Qi
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Aida Rahimi Kahmini
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA;
| | - M. Benjamin Shoemaker
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James B. Atkinson
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Thomas C. Irving
- BioCAT, Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Prescott Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Björn C. Knollmann
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jose Renato Pinto
- Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
3
|
Williams RB, Alam Afsar MN, Tikunova S, Kou Y, Fang X, Somarathne RP, Gyawu RF, Knotts GM, Agee TA, Garcia SA, Losordo LD, Fitzkee NC, Kekenes-Huskey PM, Davis JP, Johnson CN. Human disease-associated calmodulin mutations alter calcineurin function through multiple mechanisms. Cell Calcium 2023; 113:102752. [PMID: 37245392 PMCID: PMC10330910 DOI: 10.1016/j.ceca.2023.102752] [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: 12/17/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
Calmodulin (CaM) is a ubiquitous, calcium-sensing protein that regulates a multitude of processes throughout the body. In response to changes in [Ca2+], CaM modifies, activates, and deactivates enzymes and ion channels, as well as many other cellular processes. The importance of CaM is highlighted by the conservation of an identical amino acid sequence in all mammals. Alterations to CaM amino acid sequence were once thought to be incompatible with life. During the last decade modifications to the CaM protein sequence have been observed in patients suffering from life-threatening heart disease (calmodulinopathy). Thus far, inadequate or untimely interaction between mutant CaM and several proteins (LTCC, RyR2, and CaMKII) have been identified as mechanisms underlying calmodulinopathy. Given the extensive number of CaM interactions in the body, there are likely many consequences for altering CaM protein sequence. Here, we demonstrate that disease-associated CaM mutations alter the sensitivity and activity of the Ca2+-CaM-enhanced serine/threonine phosphatase calcineurin (CaN). Biophysical characterization by circular dichroism, solution NMR spectroscopy, stopped-flow kinetic measurements, and MD simulations provide mechanistic insight into mutation dysfunction as well as highlight important aspects of CaM Ca2+ signal transduction. We find that individual CaM point mutations (N53I, F89L, D129G, and F141L) impair CaN function, however, the mechanisms are not the same. Specifically, individual point mutations can influence or modify the following properties: CaM binding, Ca2+ binding, and/or Ca2+kinetics. Moreover, structural aspects of the CaNCaM complex can be altered in manners that indicate changes to allosteric transmission of CaM binding to the enzyme active site. Given that loss of CaN function can be fatal, as well as evidence that CaN modifies ion channels already associated with calmodulinopathy, our results raise the possibility that altered CaN function contributes to calmodulinopathy.
Collapse
Affiliation(s)
- Ryan B Williams
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Md Nure Alam Afsar
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Yongjun Kou
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Radha P Somarathne
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Rita F Gyawu
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Garrett M Knotts
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Taylor A Agee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Sara A Garcia
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Luke D Losordo
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A.
| | - Christopher N Johnson
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A; Vanderbilt Center for Arrhythmia Research and Therapeutics, Nashville TN 37232, U.S.A.
| |
Collapse
|
4
|
Sun B, Kekenes-Huskey PM. Calmodulin's Interdomain Linker Is Optimized for Dynamics Signal Transmission and Calcium Binding. J Chem Inf Model 2022; 62:4210-4221. [PMID: 35994621 DOI: 10.1021/acs.jcim.2c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linkers are ubiquitous in multidomain proteins. These linkers are integral to protein functions, and accumulating evidence suggests that the linkers' versatile roles are encoded in their sequences. However, a molecular picture of how amino acid differences in the linker influence protein function is still lacking. By using extensive Gaussian-accelerated MD coupled with dynamic network analysis, we reveal the molecular bases underlying the linker's role in Calmodulin (CaM), a highly conserved Ca2+-signaling hub in eukaryotes. Three CaM constructs comprising a wild-type linker, a flexible linker (four glycines at position D78-S81), and a rigid linker (four prolines at position D78-S81) were simulated. We show that the flexible linker resembles the wild type in allowing CaM to sample a large ensemble of conformations while the rigid linker confines the sampling. Our simulations recapture experimental observations that target binding enhances the Ca2+ affinity to CaM's EF-hand sites at the N-domain. However, only the wild-type linker can both correctly capture the Ca2+ binding order and maintain the α-helical structure of the domain. The other two constructs either bind Ca2+ in an incorrect order or exhibit unfolding of an N-domain helix. We demonstrate that the wild-type linker achieves these outcomes by transmitting interdomain dynamics efficiently. This was evidenced by stronger (anti)correlations among the linker residues, decoupling of the hydrogen bonds between A1-A15 and V35-E45, and structuring of the N-domain for Ca2+ binding. This decoupling was not evident for the other two constructs. Lastly, we show that the wild-type linker's optimal transmission stems from its thermodynamically favorable strain and solvation relative to the other two constructs. Our results show how the linker sequence tunes CaM function, suggesting possible mechanisms for changes in linker properties such as mutations or post-translational modifications to modulate protein/substrate binding.
Collapse
Affiliation(s)
- Bin Sun
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois 60153, United States
| |
Collapse
|