1
|
Zhuang Y, Quirk S, Stover ER, Bureau HR, Allen CR, Hernandez R. Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes. J Phys Chem B 2024; 128:2100-2113. [PMID: 38412510 PMCID: PMC10926100 DOI: 10.1021/acs.jpcb.3c08199] [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: 02/29/2024]
Abstract
The ability of antimicrobial peptides to efficiently kill their bacterial targets depends on the efficiency of their binding to the microbial membrane. In the case of enterocins, there is a three-part interaction: initial binding, unpacking of helices on the membrane surface, and permeation of the lipid bilayer. Helical unpacking is driven by disruption of the peptide hydrophobic core when in contact with membranes. Enterocin 7B is a leaderless enterocin antimicrobial peptide produced from Enterococcus faecalis that functions alone, or with its cognate partner enterocin 7A, to efficiently kill a wide variety of Gram-stain positive bacteria. To better characterize the role that tertiary structural plasticity plays in the ability of enterocin 7B to interact with the membranes, a series of arginine single-site mutants were constructed that destabilize the hydrophobic core to varying degrees. A series of experimental measures of structure, stability, and function, including CD spectra, far UV CD melting profiles, minimal inhibitory concentrations analysis, and release kinetics of calcein, show that decreased stabilization of the hydrophobic core is correlated with increased efficiency of a peptide to permeate membranes and in killing bacteria. Finally, using the computational technique of adaptive steered molecular dynamics, we found that the atomistic/energetic landscape of peptide mechanical unfolding leads to free energy differences between the wild type and its mutants, whose trends correlate well with our experiment.
Collapse
Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Erica R Stover
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hailey R Bureau
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Caley R Allen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science & Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
2
|
Cool AM, Lindert S. Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. J Chem Inf Model 2023; 63:3534-3543. [PMID: 37261389 PMCID: PMC10506665 DOI: 10.1021/acs.jcim.3c00388] [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: 06/02/2023]
Abstract
The cardiac thin filament comprises F-actin, tropomyosin, and troponin (cTn). cTn is composed of three subunits: troponin C (cTnC), troponin I (cTnI), and troponin T (cTnT). To computationally study the effect of the thin filament on cTn activation events, we employed targeted molecular dynamics followed by umbrella sampling using a model of the thin filament to measure the thermodynamics of cTn transition events. Our simulations revealed that the thin filament causes an increase in the free energy required to open the cTnC hydrophobic patch and causes a more favorable interaction between this region and the cTnI switch peptide. Mutations to the cTn complex can lead to cardiomyopathy, a collection of diseases that present clinically with symptoms of hypertrophy or dilation of the cardiac muscle, leading to impairment of the heart's ability to function normally and ultimately myocardial infarction or heart failure. Upon introduction of cardiomyopathic mutations to R145 of cTnI, we observed a general decrease in the free energy of opening the cTnC hydrophobic patch, which is on par with previous experimental results. These mutations also exhibited a decrease in electrostatic interactions between cTnI-R145 and actin-E334. After introduction of a small molecule to the wild-type cTnI-actin interface to intentionally disrupt intersubunit contacts, we successfully observed similar thermodynamic consequences and disruptions to the same protein-protein contacts as observed with the cardiomyopathic mutations. Computational studies utilizing the cTn complex in isolation would have been unable to observe these effects, highlighting the importance of using a more physiologically relevant thin-filament model to investigate the global consequences of cardiomyopathic mutations to the cTn complex.
Collapse
Affiliation(s)
- Austin M. Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| |
Collapse
|
3
|
Asencio A, Malingen S, Kooiker KB, Powers JD, Davis J, Daniel T, Moussavi-Harami F. Machine learning meets Monte Carlo methods for models of muscle's molecular machinery to classify mutations. J Gen Physiol 2023; 155:e202213291. [PMID: 37000171 PMCID: PMC10067704 DOI: 10.1085/jgp.202213291] [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: 10/31/2022] [Revised: 02/14/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
The timing and magnitude of force generation by a muscle depend on complex interactions in a compliant, contractile filament lattice. Perturbations in these interactions can result in cardiac muscle diseases. In this study, we address the fundamental challenge of connecting the temporal features of cardiac twitches to underlying rate constants and their perturbations associated with genetic cardiomyopathies. Current state-of-the-art metrics for characterizing the mechanical consequence of cardiac muscle disease do not utilize information embedded in the complete time course of twitch force. We pair dimension reduction techniques and machine learning methods to classify underlying perturbations that shape the timing of twitch force. To do this, we created a large twitch dataset using a spatially explicit Monte Carlo model of muscle contraction. Uniquely, we modified the rate constants of this model in line with mouse models of cardiac muscle disease and varied mutation penetrance. Ultimately, the results of this study show that machine learning models combined with biologically informed dimension reduction techniques can yield excellent classification accuracy of underlying muscle perturbations.
Collapse
Affiliation(s)
- Anthony Asencio
- Department of Biology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Division of Cardiology, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
| | - Sage Malingen
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
| | - Kristina B. Kooiker
- Division of Cardiology, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Joseph D. Powers
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine Pathology, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Thomas Daniel
- Department of Biology, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
| | - Farid Moussavi-Harami
- Division of Cardiology, University of Washington, Seattle, WA, USA
- Center for Transnational Muscle Research, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine Pathology, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| |
Collapse
|
4
|
Hantz ER, Lindert S. Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. J Chem Inf Model 2022; 62:6201-6208. [PMID: 36383927 PMCID: PMC10497304 DOI: 10.1021/acs.jcim.2c01132] [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: 11/17/2022]
Abstract
Calcium-dependent heart muscle contraction is regulated by the cardiac troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). cNTnC contains one calcium binding site (site II), and altered calcium binding in this site has been studied for decades. It has been previously shown that cNTnC mutants, which increase calcium sensitization may have therapeutic benefits, such as restoring cardiac muscle contractility and functionality post-myocardial infarction events. Here, we computationally characterized eight mutations for their potential effects on calcium binding affinity in site II of cNTnC. We utilized two distinct methods to estimate calcium binding: adaptive steered molecular dynamics (ASMD) and thermodynamic integration (TI). We observed a sensitizing trend for all mutations based on the employed ASMD methodology. The TI results showed excellent agreement with experimentally known calcium binding affinities in wild-type cNTnC. Based on the TI results, five mutants were predicted to increase calcium sensitivity in site II. This study presents an interesting comparison of the two computational methods, which have both been shown to be valuable tools in characterizing the impacts of calcium sensitivity in mutant cNTnC systems.
Collapse
Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
| |
Collapse
|
5
|
Cool AM, Lindert S. Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. J Chem Inf Model 2022; 62:5666-5674. [PMID: 36283742 PMCID: PMC9712266 DOI: 10.1021/acs.jcim.2c00508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cardiac troponin (cTn) complex is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the actin filament and bind to the troponin C hydrophobic patch (cTnCHP). Mutations and modifications to this complex can change its sensitivity to Ca2+ and alter the energetics of the transition from the Ca2+-unbound, cTnISP-unbound form to the Ca2+-bound, cTnISP-bound form. We utilized targeted molecular dynamics (TMD) to obtain a trajectory of this transition pathway, followed by umbrella sampling to estimate the free energy associated with the cTnISP-cTnCHP binding and the cTnCHP opening events for wild-type (WT) cTn. We were able to reproduce experimental values for the cTnISP-cTnCHP binding event and obtain cTnCHP opening free energies in agreement with previous computational measurements of smaller cTnC systems. This excellent agreement for WT cTn demonstrated the strength of computational methods in studying the dynamics and energetics of the cTn complex. We then introduced mutations to the cTn complex that cause cardiomyopathy or alter its Ca2+ sensitivity and observed a general decrease in the free energy of opening the cTnCHP. For these same mutations, we observed no general trend in the effect on the cTnISP-cTnCHP binding event. Our method sets the stage for future computational studies on this system that predict the consequences of yet uncharacterized mutations on cTn dynamics and energetics.
Collapse
Affiliation(s)
- Austin M Cool
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
6
|
Masson P, Lushchekina S. Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:6861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
Collapse
Affiliation(s)
- Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, Kremlievskaya Str. 18, 420111 Kazan, Russia
| | - Sofya Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin Str. 4, 119334 Moscow, Russia
| |
Collapse
|
7
|
Allen C, Bureau HR, McGee TD, Quirk S, Hernandez R. Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields. Chemphyschem 2022; 23:e202200175. [PMID: 35594194 PMCID: PMC9543079 DOI: 10.1002/cphc.202200175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/19/2022] [Indexed: 11/07/2022]
Abstract
The potentials of mean force (PMFs) along the end-to-end distance of two different helical peptides have been obtained and benchmarked using the adaptive steered molecular dynamics (ASMD) method. The results depend strongly on the choice of force field driving the underlying all-atom molecular dynamics, and are reported with respect to the three most popular CHARMM force field versions: c22, c27 and c36. Two small peptides, ALA 10 and 1PEF, serve as the particular case studies. The comparisons between the versions of the CHARMM force fields provides both a qualitative and quantitative look at their performance in forced unfolding simulations in which peptides undergo large changes in structural conformations. We find that ASMD with the underlying c36 force field provides the most robust results for the selected benchmark peptides.
Collapse
Affiliation(s)
- Caley Allen
- Department of ChemistryJohns Hopkins UniversityBaltimoreMD21218
| | | | | | | | - Rigoberto Hernandez
- Department of ChemistryJohns Hopkins UniversityBaltimoreMD21218
- Department of Chemical and Biomolecular Engineering, Johns Hopkins UniversityBaltimoreMD21218
- Department of Materials Science and EngineeringJohns Hopkins UniversityBaltimoreMD21218
| |
Collapse
|
8
|
Zhuang Y, Thota N, Quirk S, Hernandez R. Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2022; 18:4649-4659. [PMID: 35830368 DOI: 10.1021/acs.jctc.2c00498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala30, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.
Collapse
Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikhil Thota
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|