1
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Liu MQ, Wang BR, Qiu YC, Zhao HF, Xu SY, Yu JZ, Zhang YH, Mu ZS. Regulation and mechanism of enzyme metabolism in germinated hemp seeds by ultrasound combined with exogenous calcium chloride treatment. Int J Biol Macromol 2024; 276:133732. [PMID: 39002919 DOI: 10.1016/j.ijbiomac.2024.133732] [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: 03/12/2024] [Revised: 06/26/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
γ-aminobutyric acid (GABA) plays an important role in anti-anxiety by inhibiting neurotransmitter in the central nervous system (CNS) of mammals, which is generated in the germinating seeds. The key enzymes activity of GABA metabolism pathway and nutrients content in hemp seeds during germination were studied after treated with ultrasound and CaCl2. The mechanism of exogenous stress on key enzymes in GABA metabolism pathway was investigated by molecular dynamics simulation. The results showed that ultrasonic combined with 1.5 mmol·L-1CaCl2 significantly increased the activities of glutamate decarboxylase (GAD) and GABA transaminase (GABA-T) in seeds, and promoted the conversion of glutamate to GABA, resulting in the decrease of glutamate content and the accumulation of GABA. Molecular dynamics simulations revealed that Ca2+ environment enhanced the activity of GAD and GABA-T enzymes by altering their secondary structure, exposing their hydrophobic residues. Ultrasound, germination and CaCl2 stress improved the nutritional value of hemp seeds.
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Affiliation(s)
- Meng-Qi Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Bao-Rong Wang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying-Chao Qiu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Hong-Fu Zhao
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Shi-Yao Xu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Jing-Zhi Yu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying-Hua Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
| | - Zhi-Shen Mu
- Inner Mongolia Enterprise Key Laboratory of Dairy Nutrition, Health & Safety, Inner Mongolia Mengniu Dairy (Group) Co., Ltd., Huhhot 011500, PR China.
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2
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Greene D, Barton M, Luchko T, Shiferaw Y. Computational Analysis of Binding Interactions between the Ryanodine Receptor Type 2 and Calmodulin. J Phys Chem B 2021; 125:10720-10735. [PMID: 34533024 DOI: 10.1021/acs.jpcb.1c03896] [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
Mutations in the cardiac ryanodine receptor type 2 (RyR2) have been linked to a variety of cardiac arrhythmias, such as catecholaminergic polymorphic ventricular tachycardia (CPVT). RyR2 is regulated by calmodulin (CaM), and mutations that disrupt their interaction can cause aberrant calcium release, leading to an arrhythmia. It was recently shown that increasing the RyR2-CaM binding affinity could rescue a defective CPVT-related RyR2 channel to near wild-type behavior. However, the interactions that determine the binding affinity at the RyR2-CaM binding interface are not well understood. In this study, we identify the key domains and interactions, including several new interactions, involved in the binding of CaM to RyR2. Also, our comparison between the wild-type and V3599K mutant suggests how the RyR2-CaM binding affinity can be increased via a change in the central and N-terminal lobe binding contacts for CaM. This computational approach provides new insights into the effect of a mutation at the RyR2-CaM binding interface, and it may find utility in drug design for the future treatment of cardiac arrhythmias.
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Affiliation(s)
- D'Artagnan Greene
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Michael Barton
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Tyler Luchko
- Department of Physics, California State University, Northridge, California 91330, United States
| | - Yohannes Shiferaw
- Department of Physics, California State University, Northridge, California 91330, United States
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3
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Nde J, Zhang P, Ezerski JC, Lu W, Knapp K, Wolynes PG, Cheung MS. Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca 2+-Calmodulin. Front Mol Biosci 2021; 8:661322. [PMID: 34504868 PMCID: PMC8421859 DOI: 10.3389/fmolb.2021.661322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022] Open
Abstract
Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca2+), or vice versa, may provide insight into how Ca2+-CaM selects its target binding proteins. However, modeling of Ca2+-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the two lobes are relatively rigid due to tight binding of the Ca2+ to the calcium-binding loops where the loop forms a pentagonal bipyramidal coordination geometry with Ca2+. This feature that underlies the reciprocal relation between Ca2+ binding and target binding of CaM, however, has yet to be considered in the structural modeling. Here, we presented a coarse-grained model based on the Associative memory, Water mediated, Structure, and Energy Model (AWSEM) protein force field, to investigate the salient features of CaM. Particularly, we optimized the force field of CaM and that of Ca2+ ions by using its coordination chemistry in the calcium-binding loops to match with experimental observations. We presented a “community model” of CaM that is capable of sampling various conformations of CaM, incorporating various calcium-binding states, and carrying the memory of binding with various targets, which sets the foundation of the reciprocal relation of target binding and Ca2+ binding in future studies.
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Affiliation(s)
- Jules Nde
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Pengzhi Zhang
- Department of Physics, University of Houston, Houston, TX, United States
| | - Jacob C Ezerski
- Department of Physics, University of Houston, Houston, TX, United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Kaitlin Knapp
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
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4
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Sun B, Kekenes-Huskey PM. Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. Int J Mol Sci 2021; 22:ijms22094990. [PMID: 34066691 PMCID: PMC8125811 DOI: 10.3390/ijms22094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet. Insights into this would be invaluable to understanding its regulation of diverse cellular signaling pathways. Therefore, we utilized Martini coarse-grained (CG) molecular dynamics simulations to probe CaM/target assembly for a model system: CaM binding to the calcineurin (CaN) regulatory domain. The simulations were conducted assuming a ‘wild-type’ calmodulin with normal flexibility of its linker, as well as a labile, highly-flexible linker variant to emulate structural changes that could be induced, for instance, by post-translational modifications. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in the experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 × 108 M−1 s−1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 × 108 M−1 s−1. Furthermore, our simulations recapitulated its well-known inverse relationship between the association rate and the solution ionic strength. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration. This effect appears to stem from a difference in the ensembles of extended and collapsed states which are controlled by the linker flexibility. Therefore, our simulations suggest that variations in the CaM linker’s propensity for alpha helical secondary structure can modulate the kinetics of target binding.
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5
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Pitard I, Monet D, Goossens PL, Blondel A, Malliavin TE. Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin. Front Mol Biosci 2020; 7:586544. [PMID: 33344505 PMCID: PMC7746812 DOI: 10.3389/fmolb.2020.586544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022] Open
Abstract
Molecular dynamics (MD) simulations have been recorded on the complex between the edema factor (EF) of Bacilllus anthracis and calmodulin (CaM), starting from a structure with the orthosteric inhibitor adefovir bound in the EF catalytic site. The starting structure has been destabilized by alternately suppressing different co-factors, such as adefovir ligand or ions, revealing several long-distance correlations between the conformation of CaM, the geometry of the CaM/EF interface, the enzymatic site and the overall organization of the complex. An allosteric communication between CaM/EF interface and the EF catalytic site, highlighted by these correlations, was confirmed by several bioinformatics approaches from the literature. A network of hydrogen bonds and stacking interactions extending from the helix V of of CaM, and the residues of the switches A, B and C, and connecting to catalytic site residues, is a plausible candidate for the mediation of allosteric communication. The greatest variability in volume between the different MD conditions was also found for cavities present at the EF/CaM interface and in the EF catalytic site. The similarity between the predictions from literature and the volume variability might introduce the volume variability as new descriptor of allostery.
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France.,Ecole Doctorale Université Paris Sorbonne, Paris, France
| | - Damien Monet
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France.,Ecole Doctorale Université Paris Sorbonne, Paris, France
| | | | - Arnaud Blondel
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France
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6
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Bappy SS, Sultana S, Adhikari J, Mahmud S, Khan MA, Kibria KMK, Rahman MM, Shibly AZ. Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach. J Biomol Struct Dyn 2020; 39:1139-1154. [PMID: 32037968 DOI: 10.1080/07391102.2020.1726815] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chikungunya virus (CHIKV) instigating Chikungunya fever is a global infective menace resulting in high fever, weakened joint-muscle pain, and brain inflammation. Inaccessibility and unavailability of effective drugs have led us to an uncertain arena when it comes to providing proper medical treatment to the affected people. In this study, authentic encroachment has been made concerning the peptide-based epitope vaccine designing against CHIKV. A Proteome-wide search was performed to locate a conserved portion among the accessible viral outer membrane proteins which showcase a remarkable immune response using specific immunoinformatics and docking simulation tools. Primarily, the most probable immunogenic envelope glycoproteins E1 and E2 were identified from the UniProt database depending on their antigenicity scores. Subsequently, we selected two distinctive sequences "SEDVYANTQLVLQRP" and "IMLLYPDHPTLLSYR" in both E1 and E2 glycoproteins respectively. These two sequences identified as the most potent T and B cell epitope-based peptides as they interacted with 6 and 7 HLA-I and 5 HLA-II molecules with an extremely low IC50 score that was verified by molecular docking. Moreover, the sequences possess no allergenicity and are certainly located outside the transmembrane region. In addition, the sequences exhibited 88.46% and 100.00% Conservancy, covering high population coverage of 89.49% to 94.74% and 60.51% to 88.87% respectively in endemic countries. The identified peptide SEDVYANTQLVLQRP and IMLLYPDHPTLLSYR can be utilized next for the development of peptide-based epitope vaccine contrary to CHIKV, so further documentations and experimentations like Antigen testing, Antigen production, Clinical trials are needed to prove the validity of it. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Shahariar Bappy
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Sorna Sultana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Juthi Adhikari
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh.,Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, Dhaka, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Abu Zaffar Shibly
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
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7
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Pitard I, Malliavin TE. Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells. Toxins (Basel) 2019; 11:toxins11060369. [PMID: 31238550 PMCID: PMC6628625 DOI: 10.3390/toxins11060369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the functions and mechanisms of biological systems is an outstanding challenge. One way to overcome it is to combine together several approaches such as molecular modeling and experimental structural biology techniques. Indeed, the interplay between structural and dynamical properties of the system is crucial to unravel the function of molecular machinery’s. In this review, we focus on how molecular simulations along with structural information can aid in interpreting biological data. Here, we examine two different cases: (i) the endosomal translocation toxins (diphtheria, tetanus, botulinum toxins) and (ii) the activation of adenylyl cyclase inside the cytoplasm (edema factor, CyA, ExoY).
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005 Paris, France.
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
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8
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Zhang P, Tripathi S, Trinh H, Cheung MS. Opposing Intermolecular Tuning of Ca 2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides. Biophys J 2017; 112:1105-1119. [PMID: 28355539 PMCID: PMC5374985 DOI: 10.1016/j.bpj.2017.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13–49), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng13–49 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13–49 structures by matching the changes in the chemical shifts of CaM upon Ng13–49 binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng13–49 by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+ release. In contrast, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13–49 and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca2+ binding affinities.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas
| | | | - Hoa Trinh
- Department of Physics, University of Houston, Houston, Texas
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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9
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Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics. Toxins (Basel) 2017; 9:toxins9070199. [PMID: 28672846 PMCID: PMC5535146 DOI: 10.3390/toxins9070199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/16/2022] Open
Abstract
Although CyaA has been studied for over three decades and revealed itself to be a very good prototype for developing various biotechnological applications, only a little is known about its functional dynamics and about the conformational landscape of this protein. Molecular dynamics simulations helped to clarify the view on these points in the following way. First, the model of interaction between AC and calmodulin (CaM) has evolved from an interaction centered on the surface between C-CaM hydrophobic patch and the α helix H of AC, to a more balanced view, in which the C-terminal tail of AC along with the C-CaM Calcium loops play an important role. This role has been confirmed by the reduction of the affinity of AC for calmodulin in the presence of R338, D360 and N347 mutations. In addition, enhanced sampling studies have permitted to propose a representation of the conformational space for the isolated AC. It remains to refine this representation using structural low resolution information measured on the inactive state of AC. Finally, due to a virtual screening study on another adenyl cyclase from Bacillus anthracis, weak inhibitors of AC have been discovered.
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10
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Feng M, Bell DR, Luo J, Zhou R. Impact of graphyne on structural and dynamical properties of calmodulin. Phys Chem Chem Phys 2017; 19:10187-10195. [PMID: 28374026 DOI: 10.1039/c7cp00720e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbon-based nanomaterials such as graphyne, graphene, and carbon nanotubes have attracted considerable attention for their applications, but questions remain regarding their biosafety through potential adverse interactions with important biomolecules.
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Affiliation(s)
- Mei Feng
- Department of Physics
- Institute of Quantitative Biology
- Zhejiang University
- Hangzhou
- China
| | - David R. Bell
- Computational Biological Center
- IBM Thomas J. Watson Research Center
- Yorktown Heights
- USA
| | - Judong Luo
- Department of Oncology
- The Affiliated Hospital of Nanjing Medical University
- Changzhou No. 2 People's Hospital
- Changzhou
- China
| | - Ruhong Zhou
- Department of Physics
- Institute of Quantitative Biology
- Zhejiang University
- Hangzhou
- China
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11
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Molecular Basis of S100A1 Activation at Saturating and Subsaturating Calcium Concentrations. Biophys J 2016; 110:1052-63. [PMID: 26958883 DOI: 10.1016/j.bpj.2015.12.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022] Open
Abstract
The S100A1 protein mediates a wide variety of physiological processes through its binding of calcium (Ca(2+)) and endogenous target proteins. S100A1 presents two Ca(2+)-binding domains: a high-affinity "canonical" EF (cEF) hand and a low-affinity "pseudo" EF (pEF) hand. Accumulating evidence suggests that both Ca(2+)-binding sites must be saturated to stabilize an open state conducive to peptide recognition, yet the pEF hand's low affinity limits Ca(2+) binding at normal physiological concentrations. To understand the molecular basis of Ca(2+) binding and open-state stabilization, we performed 100 ns molecular dynamics simulations of S100A1 in the apo/holo (Ca(2+)-free/bound) states and a half-saturated state, for which only the cEF sites are Ca(2+)-bound. Our simulations indicate that the pattern of oxygen coordination about Ca(2+) in the cEF relative to the pEF site contributes to the former's higher affinity, whereas Ca(2+) binding strongly reshapes the protein's conformational dynamics by disrupting β-sheet coupling between EF hands. Moreover, modeling of the half-saturated configuration suggests that the open state is unstable and reverts toward a closed state in the absence of the pEF Ca(2+) ion. These findings indicate that Ca(2+) binding at the cEF site alone is insufficient to stabilize opening; thus, posttranslational modification of the protein may be required for target peptide binding at subsaturating intracellular Ca(2+) levels.
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12
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Calmodulin interacts with Rab3D and modulates osteoclastic bone resorption. Sci Rep 2016; 6:37963. [PMID: 27897225 PMCID: PMC5126571 DOI: 10.1038/srep37963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/03/2016] [Indexed: 11/09/2022] Open
Abstract
Calmodulin is a highly versatile protein that regulates intracellular calcium homeostasis and is involved in a variety of cellular functions including cardiac excitability, synaptic plasticity and signaling transduction. During osteoclastic bone resorption, calmodulin has been reported to concentrate at the ruffled border membrane of osteoclasts where it is thought to modulate bone resorption activity in response to calcium. Here we report an interaction between calmodulin and Rab3D, a small exocytic GTPase and established regulator osteoclastic bone resorption. Using yeast two-hybrid screening together with a series of protein-protein interaction studies, we show that calmodulin interacts with Rab3D in a calcium dependent manner. Consistently, expression of a calcium insensitive form of calmodulin (i.e. CaM1234) perturbs calmodulin-Rab3D interaction as monitored by bioluminescence resonance energy transfer (BRET) assays. In osteoclasts, calmodulin and Rab3D are constitutively co-expressed during RANKL-induced osteoclast differentiation, co-occupy plasma membrane fractions by differential gradient sedimentation assay and colocalise in the ruffled border as revealed by confocal microscopy. Further, functional blockade of calmodulin-Rab3D interaction by calmidazolium chloride coincides with an attenuation of osteoclastic bone resorption. Our data imply that calmodulin- Rab3D interaction is required for efficient bone resorption by osteoclasts in vitro.
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13
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Makiyama RK, Fernandes CAH, Dreyer TR, Moda BS, Matioli FF, Fontes MRM, Maia IG. Structural and thermodynamic studies of the tobacco calmodulin-like rgs-CaM protein. Int J Biol Macromol 2016; 92:1288-1297. [PMID: 27514444 DOI: 10.1016/j.ijbiomac.2016.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/08/2016] [Accepted: 08/07/2016] [Indexed: 11/23/2022]
Abstract
The tobacco calmodulin-like protein rgs-CaM is involved in host defense against virus and is reported to possess an associated RNA silencing suppressor activity. Rgs-CaM is also believed to act as an antiviral factor by interacting and targeting viral silencing suppressors for autophagic degradation. Despite these functional data, calcium interplay in the modulation of rgs-CaM is still poorly understood. Here we show that rgs-CaM displays a prevalent alpha-helical conformation and possesses three functional Ca2+-binding sites. Using computational modeling and molecular dynamics simulation, we demonstrate that Ca2+ binding to rgs-CaM triggers expansion of its tertiary structure with reorientation of alpha-helices within the EF-hands. This conformational change leads to the exposure of a large negatively charged region that may be implicated in the electrostatic interactions between rgs-CaM and viral suppressors. Moreover, the kd values obtained for Ca2+ binding to the three functional sites are not within the affinity range of a typical Ca2+ sensor.
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Affiliation(s)
- Rodrigo K Makiyama
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil
| | - Carlos A H Fernandes
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Bruno S Moda
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil
| | - Fabio F Matioli
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Ivan G Maia
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil.
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14
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Tripathi S, Wang Q, Zhang P, Hoffman L, Waxham MN, Cheung MS. Conformational frustration in calmodulin-target recognition. J Mol Recognit 2015; 28:74-86. [PMID: 25622562 DOI: 10.1002/jmr.2413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
Calmodulin (CaM) is a primary calcium (Ca(2+) )-signaling protein that specifically recognizes and activates highly diverse target proteins. We explored the molecular basis of target recognition of CaM with peptides representing the CaM-binding domains from two Ca(2+) -CaM-dependent kinases, CaMKI and CaMKII, by employing experimentally constrained molecular simulations. Detailed binding route analysis revealed that the two CaM target peptides, although similar in length and net charge, follow distinct routes that lead to a higher binding frustration in the CaM-CaMKII complex than in the CaM-CaMKI complex. We discovered that the molecular origin of the binding frustration is caused by intermolecular contacts formed with the C-domain of CaM that need to be broken before the formation of intermolecular contacts with the N-domain of CaM. We argue that the binding frustration is important for determining the kinetics of the recognition process of proteins involving large structural fluctuations.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Physics, University of Houston, Houston, TX, 77204, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
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15
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Abstract
This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.
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Affiliation(s)
- Krzysztof Kuczera
- Departments of Chemistry and Molecular Biosciences, University of Kansas, 1251 Wescoe Hall Drive, Room 5090, Lawrence, KS, 66045, USA,
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16
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Gao J, Wang L, Kang SG, Zhao L, Ji M, Chen C, Zhao Y, Zhou R, Li J. Size-dependent impact of CNTs on dynamic properties of calmodulin. NANOSCALE 2014; 6:12828-37. [PMID: 25225777 DOI: 10.1039/c4nr01623h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
There are growing concerns about the biosafety of nanomaterials such as carbon nanotubes (CNTs) as their applications become more widespread. We report here a theoretical and experimental study of the binding of various sizes of CNTs [CNT (4,4), (5,5), (6,6) and (7,7)] to calmodulin (CaM) protein and, in particular, their impact on the Ca(2+)-dependent dynamic properties of CaM. Our simulations show that all the CNTs can plug into the hydrophobic binding pocket of Ca(2+)-bound CaM with binding affinities comparable with the native substrate M13 peptide. Even though CNT (4,4) shows a similar behavior to the M13 peptide in its dissociation from Ca(2+)-free CaM, wider CNTs still bind firmly to CaM, indicating a potential failure of Ca(2+) regulation. Such a size-dependent impact of CNTs on the dynamic properties of CaM is a result of the excessively strong hydrophobic interactions between the wider CNTs and CaM. These simulation results were confirmed by circular dichroism spectroscopy, which showed that the secondary structures of CaM become insensitive to Ca(2+) concentrations after the addition of CNTs. Our findings indicate that the cytotoxicity of nanoparticles to proteins arises not only from the inhibition of static protein structures (binding pockets), but also from impacts on their dynamic properties.
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Affiliation(s)
- Jian Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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17
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González-Andrade M, Mata R, Madariaga-Mazón A, Rodríguez-Sotres R, Del Pozo-Yauner L, Sosa-Peinado A. Importance of the interaction protein-protein of the CaM-PDE1A and CaM-MLCK complexes in the development of new anti-CaM drugs. J Mol Recognit 2013; 26:165-74. [PMID: 23456740 DOI: 10.1002/jmr.2261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 11/16/2012] [Accepted: 12/12/2012] [Indexed: 11/07/2022]
Abstract
Protein-protein interactions play central roles in physiological and pathological processes. The bases of the mechanisms of drug action are relevant to the discovery of new therapeutic targets. This work focuses on understanding the interactions in protein-protein-ligands complexes, using proteins calmodulin (CaM), human calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A active human (PDE1A), and myosin light chain kinase (MLCK) and ligands αII-spectrin peptide (αII-spec), and two inhibitors of CaM (chlorpromazine (CPZ) and malbrancheamide (MBC)). The interaction was monitored with a fluorescent biosensor of CaM (hCaM M124C-mBBr). The results showed changes in the affinity of CPZ and MBC depending on the CaM-protein complex under analysis. For the Ca(2+) -CaM, Ca(2+) -CaM-PDE1A, and Ca(2+) -CaM-MLCK complexes, CPZ apparent dissociation constants (Kds ) were 1.11, 0.28, and 0.55 μM, respectively; and for MBC Kds were 1.43, 1.10, and 0.61 μM, respectively. In competition experiments the addition of calmodulin binding peptide 1 (αII-spec) to Ca(2+) -hCaM M124C-mBBr quenched the fluorescence (Kd = 2.55 ± 1.75 pM) and the later addition of MBC (up to 16 μM) did not affect the fluorescent signal. Instead, the additions of αII-spec to a preformed Ca(2+) -hCaM M124C-mBBr-MBC complex modified the fluorescent signal. However, MBC was able to displace the PDE1A and MLCK from its complex with Ca(2+) -CaM. In addition, docking studies were performed for all complexes with both ligands showing an excellent correlation with experimental data. These experiments may help to explain why in vivo many CaM drugs target prefer only a subset of the Ca(2+) -CaM regulated proteins and adds to the understanding of molecular interactions between protein complexes and small ligands.
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18
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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19
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Smith DMA, Straatsma TP, Squier TC. Retention of conformational entropy upon calmodulin binding to target peptides is driven by transient salt bridges. Biophys J 2012; 103:1576-84. [PMID: 23062350 DOI: 10.1016/j.bpj.2012.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/06/2012] [Accepted: 08/17/2012] [Indexed: 10/27/2022] Open
Abstract
Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable binding sequences in target proteins. To identify how binding affects CaM motions, and its relationship to conformational entropy and target peptide sequence, we have employed fully atomistic, explicit solvent molecular dynamics simulations of unbound CaM and CaM bound to five different target peptides. The calculated CaM conformational binding entropies correlate with experimentally derived conformational entropies with a correlation coefficient R(2) of 0.95. Selected side-chain interactions with target peptides restrain interhelical loop motions, acting to tune the conformational entropy of the bound complex via widely distributed CaM motions. In the complex with the most conformational entropy retention (CaM in complex with the neuronal nitric oxide synthase binding sequence), Lys-148 at the C-terminus of CaM forms transient salt bridges alternating between Glu side chains in the N-domain, the central linker, and the binding target. Additional analyses of CaM structures, fluctuations, and CaM-target interactions illuminate the interplay between electrostatic, side chain, and backbone properties in the ability of CaM to recognize and discriminate against targets by tuning its conformational entropy, and suggest a need to consider conformational dynamics in optimizing binding affinities.
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20
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Li H, Wells SA, Jimenez-Roldan JE, Römer RA, Zhao Y, Sadler PJ, O'Connor PB. Protein flexibility is key to cisplatin crosslinking in calmodulin. Protein Sci 2012; 21:1269-79. [PMID: 22733664 PMCID: PMC3631356 DOI: 10.1002/pro.2111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/15/2012] [Indexed: 01/03/2023]
Abstract
Chemical crosslinking in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) has significant potential for studying protein structures and protein-protein interactions. Previously, cisplatin has been shown to be a crosslinker and crosslinks multiple methionine (Met) residues in apo-calmodulin (apo-CaM). However, the inter-residue distances obtained from nuclear magnetic resonance structures are inconsistent with the measured distance constraints by crosslinking. Met residues lie too far apart to be crosslinked by cisplatin. Here, by combining FTICR MS with a novel computational flexibility analysis, the flexible nature of the CaM structure is found to be key to cisplatin crosslinking in CaM. It is found that the side chains of Met residues can be brought together by flexible motions in both apo-CaM and calcium-bound CaM (Ca₄-CaM). The possibility of cisplatin crosslinking Ca₄-CaM is then confirmed by MS data. Therefore, flexibility analysis as a fast and low-cost computational method can be a useful tool for predicting crosslinking pairs in protein crosslinking analysis and facilitating MS data analysis. Finally, flexibility analysis also indicates that the crosslinking of platinum to pairs of Met residues will effectively close the nonpolar groove and thus will likely interfere with the binding of CaM to its protein targets, as was proved by comparing assays for cisplatin-modified/unmodified CaM binding to melittin. Collectively, these results suggest that cisplatin crosslinking of apo-CaM or Ca₄-CaM can inhibit the ability of CaM to recognize its target proteins, which may have important implications for understanding the mechanism of tumor resistance to platinum anticancer drugs.
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Affiliation(s)
- Huilin Li
- Department of Chemistry, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - Stephen A Wells
- Department of Physics and Centre for Scientific Computing, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - J Emilio Jimenez-Roldan
- Department of Physics and Centre for Scientific Computing, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - Rudolf A Römer
- Department of Physics and Centre for Scientific Computing, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - Yao Zhao
- Department of Chemistry, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - Peter J Sadler
- Department of Chemistry, University of WarwickCoventry, CV4 7AL, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of WarwickCoventry, CV4 7AL, United Kingdom
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21
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Kuczera K, Kursula P. Interactions of calmodulin with death-associated protein kinase peptides: experimental and modeling studies. J Biomol Struct Dyn 2012; 30:45-61. [PMID: 22571432 DOI: 10.1080/07391102.2012.674221] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have studied the interactions between calmodulin (CaM) and three target peptides from the death-associated protein kinase (DAPK) protein family using both experimental and modeling methods, aimed at determining the details of the underlying biological regulation mechanisms. Experimentally, calorimetric binding free energies were determined for the complexes of CaM with peptides representing the DAPK2 wild-type and S308D mutant, as well as DAPK1. The observed affinity of CaM was very similar for all three studied peptides. The DAPK2 and DAPK1 peptides differ significantly in sequence and total charge, while the DAPK2 S308D mutant is designed to model the effects of DAPK2 Ser308 phosphorylation. The crystal structure of the CaM-DAPK2 S308D mutant peptide is also reported. The structures of CaM-DAPK peptide complexes present a mode of CaM-kinase interaction, in which bulky hydrophobic residues at positions 10 and 14 are both bound to the same hydrophobic cleft. To explain the microscopic effects underlying these interactions, we performed free energy calculations based on the approximate MM-PBSA approach. For these highly charged systems, standard MM-PBSA calculations did not yield satisfactory results. We proposed a rational modification of the approach which led to reasonable predictions of binding free energies. All three complexes are strongly stabilized by two effects: electrostatic interactions and buried surface area. The strong favorable interactions are to a large part compensated by unfavorable entropic terms, in which vibrational entropy is the largest contributor. The electrostatic component of the binding free energy followed the trend of the overall peptide charge, with strongest interactions for DAPK1 and weakest for the DAPK2 mutant. The electrostatics was dominated by interactions of the positively charged residues of the peptide with the negatively charged residues of CaM. The nonpolar binding free energy was comparable for all three peptides, the largest contribution coming from the Trp305. About two-thirds of the buried surface area corresponds to nonpolar residues, showing that hydrophobic interactions play an important role in these CaM-peptide complexes. The simulation results agree with the experimental data in predicting a small effect of the S308D mutation on CaM interactions with DAPK2, suggesting that this mutation is not a good model for the S308 phosphorylation.
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Affiliation(s)
- Krzysztof Kuczera
- Departments of Chemistry and Biochemistry, University of Kansas, Lawrence, KS, 66045, USA.
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22
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Laine É, Martínez L, Ladant D, Malliavin T, Blondel A. Molecular motions as a drug target: mechanistic simulations of anthrax toxin edema factor function led to the discovery of novel allosteric inhibitors. Toxins (Basel) 2012; 4:580-604. [PMID: 23012649 PMCID: PMC3446745 DOI: 10.3390/toxins4080580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 01/14/2023] Open
Abstract
Edema Factor (EF) is a component of Bacillus anthracis toxin essential for virulence. Its adenylyl cyclase activity is induced by complexation with the ubiquitous eukaryotic cellular protein, calmodulin (CaM). EF and its complexes with CaM, nucleotides and/or ions, have been extensively characterized by X-ray crystallography. Those structural data allowed molecular simulations analysis of various aspects of EF action mechanism, including the delineation of EF and CaM domains through their association energetics, the impact of calcium binding on CaM, and the role of catalytic site ions. Furthermore, a transition path connecting the free inactive form to the CaM-complexed active form of EF was built to model the activation mechanism in an attempt to define an inhibition strategy. The cavities at the surface of EF were determined for each path intermediate to identify potential sites where the binding of a ligand could block activation. A non-catalytic cavity (allosteric) was found to shrink rapidly at early stages of the path and was chosen to perform virtual screening. Amongst 18 compounds selected in silico and tested in an enzymatic assay, 6 thiophen ureidoacid derivatives formed a new family of EF allosteric inhibitors with IC50 as low as 2 micromolars.
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Affiliation(s)
- Élodie Laine
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France;
| | - Leandro Martínez
- The Molecular Biotechnology Group, Institute of Physics of São Carlos, University of São Paulo, Av. Trabalhador Sãocarlense, 400, 13566-590 São Carlos, SP, Brazil;
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 28, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Thérèse Malliavin
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
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23
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Identification of the critical structural determinants of the EF-hand domain arrangements in calcium binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:608-19. [PMID: 22285364 DOI: 10.1016/j.bbapap.2012.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 12/02/2011] [Accepted: 01/04/2012] [Indexed: 11/22/2022]
Abstract
EF-hand calcium binding proteins (CaBPs) share strong sequence homology, but exhibit great diversity in structure and function. Thus although calmodulin (CaM) and calcineurin B (CNB) both consist of four EF hands, their domain arrangements are quite distinct. CaM and the CaM-like proteins are characterized by an extended architecture, whereas CNB and the CNB-like proteins have a more compact form. In this study, we performed structural alignments and molecular dynamics (MD) simulations on 3 CaM-like proteins and 6 CNB-like proteins, and quantified their distinct structural and dynamical features in an effort to establish how their sequences specify their structures and dynamics. Alignments of the EF2-EF3 region of these proteins revealed that several residues (not restricted to the linker between the EF2 and EF3 motifs) differed between the two groups of proteins. A customized inverse folding approach followed by structural assessments and MD simulations established the critical role of these residues in determining the structure of the proteins. Identification of the critical determinants of the two different EF-hand domain arrangements and the distinct dynamical features relevant to their respective functions provides insight into the relationships between sequence, structure, dynamics and function among these EF-hand CaBPs.
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24
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Selwa E, Laine E, Malliavin TE. Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis. Proteins 2012; 80:1028-40. [DOI: 10.1002/prot.24005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Revised: 11/04/2011] [Accepted: 11/14/2011] [Indexed: 11/10/2022]
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25
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The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLoS Comput Biol 2011; 7:e1002114. [PMID: 21829336 PMCID: PMC3145654 DOI: 10.1371/journal.pcbi.1002114] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/23/2011] [Indexed: 11/20/2022] Open
Abstract
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.
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26
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Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners. J Mol Biol 2011; 411:713-27. [PMID: 21723293 DOI: 10.1016/j.jmb.2011.06.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 05/18/2011] [Accepted: 06/15/2011] [Indexed: 11/20/2022]
Abstract
Cellular functions of an organism are maintained by protein-protein interactions. Those proteins that bind multiple partners asynchronously (date hub proteins) are important to make the interaction network coordinated. It is known that many date hub proteins bind different partners at overlapping (OV) interfaces. To understand how OV interfaces of date hub proteins can recognize multiple partners, we analyzed the difference between OV and non-overlapping (Non-OV) regions of interfaces involved in the binding of different partners. By using the structures of 16 date hub proteins with various interaction partners (ranging from 5 to 33), we compared buried surface area, compositions of amino acid residues and secondary structures, and side-chain orientations. It was found that buried interface residues are important for recognizing multiple partners, while exposed interface residues are important for determining specificity to a particular ligand. In addition, our analyses reveal that residue compositions in OV and Non-OV regions are different and that residues in OV region show diverse side-chain torsion angles to accommodate binding to multiple targets.
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27
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Laine E, Martínez L, Blondel A, Malliavin TE. Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding. Biophys J 2011; 99:2264-72. [PMID: 20923661 DOI: 10.1016/j.bpj.2010.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/14/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Calmodulin (CaM) is a remarkably flexible protein which can bind multiple targets in response to changes in intracellular calcium concentration. It contains four calcium-binding sites, arranged in two globular domains. The calcium affinity of CaM N-terminal domain (N-CaM) is dramatically reduced when the complex with the edema factor (EF) of Bacillus anthracis is formed. Here, an atomic explanation for this reduced affinity is proposed through molecular dynamics simulations and free energy perturbation calculations of the EF-CaM complex starting from different crystallographic models. The simulations show that electrostatic interactions between CaM and EF disfavor the opening of N-CaM domains usually induced by calcium binding. Relative calcium affinities of the N-CaM binding sites are probed by free energy perturbation, and dissociation probabilities are evaluated with locally enhanced sampling simulations. We show that EF impairs calcium binding on N-CaM through a direct conformational restraint on Site 1, by an indirect destabilization of Site 2, and by reducing the cooperativity between the two sites.
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Affiliation(s)
- Elodie Laine
- Unité de Bioinformatique Structurale, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France.
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28
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Bigelow DJ, Squier TC. Thioredoxin-dependent redox regulation of cellular signaling and stress response through reversible oxidation of methionines. MOLECULAR BIOSYSTEMS 2011; 7:2101-9. [DOI: 10.1039/c1mb05081h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Homouz D, Sanabria H, Waxham MN, Cheung MS. Modulation of calmodulin plasticity by the effect of macromolecular crowding. J Mol Biol 2009; 391:933-43. [PMID: 19577574 DOI: 10.1016/j.jmb.2009.06.073] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 06/24/2009] [Accepted: 06/28/2009] [Indexed: 11/20/2022]
Abstract
In vitro biochemical reactions are most often studied in dilute solution, a poor mimic of the intracellular space of eukaryotic cells, which are crowded with mobile and immobile macromolecules. Such crowded conditions exert volume exclusion and other entropic forces that have the potential to impact chemical equilibria and reaction rates. In this article, we used the well-characterized and ubiquitous molecule calmodulin (CaM) and a combination of theoretical and experimental approaches to address how crowding impacts CaM's conformational plasticity. CaM is a dumbbell-shaped molecule that contains four EF hands (two in the N-lobe and two in the C-lobe) that each could bind Ca(2+), leading to stabilization of certain substates that favor interactions with other target proteins. Using coarse-grained molecular simulations, we explored the distribution of CaM conformations in the presence of crowding agents. These predictions, in which crowding effects enhance the population of compact structures, were then confirmed in experimental measurements using fluorescence resonance energy transfer techniques of donor- and acceptor-labeled CaM under normal and crowded conditions. Using protein reconstruction methods, we further explored the folding-energy landscape and examined the structural characteristics of CaM at free-energy basins. We discovered that crowding stabilizes several different compact conformations, which reflects the inherent plasticity in CaM's structure. From these results, we suggest that the EF hands in the C-lobe are flexible and can be thought of as a switch, while those in the N-lobe are stiff, analogous to a rheostat. New combinatorial signaling properties may arise from the product of the differential plasticity of the two distinct lobes of CaM in the presence of crowding. We discuss the implications of these results for modulating CaM's ability to bind Ca(2+) and target proteins.
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Affiliation(s)
- Dirar Homouz
- Department of Physics, University of Houston, TX 77204, USA
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30
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Laine E, Blondel A, Malliavin TE. Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex. Biophys J 2009; 96:1249-63. [PMID: 19217845 DOI: 10.1016/j.bpj.2008.10.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 10/21/2008] [Indexed: 01/03/2023] Open
Abstract
We have studied the relationship between dynamical correlations and energetic contributions in an attempt to model the transmission of information inside protein-protein complexes. The complex formed between the edema factor (EF) of Bacillus anthracis and calmodulin (CaM) was taken as an example, as the formation and stability of the complex depend on the calcium complexation level. The effect of calcium through EF-CaM residue network has been investigated with various approaches: 1), the elastic network model; 2), the local feature analysis; 3), the generalized correlations; and 4), the energetic dependency maps (EDMs), on 15-ns molecular dynamics simulations of the complex loaded with 0, 2, or 4 Ca2+ ions. The elastic network model correctly describes the basic architecture of the complex but is poorly sensitive to the level of calcium compared to the other methods. The local feature analysis allows us to characterize the local dynamics of the complex and the propagation of the calcium signal through CaM. The analyses of global dynamics and energetics--through generalized correlations and EDMs--provide a comprehensive picture of EF-CaM architecture and can be unified by using the concept of residue network connectedness. A medium connectedness, defined as the ability of each residue to communicate with all remaining parts of the complex, is observed for the 2Ca2+ level, which was experimentally identified as the most stable form of EF-CaM. The hierarchy of relative stabilities given by the EDMs sheds a new light on the EF-CaM interaction mechanism described experimentally and supports an organization of the complex architecture centered around nucleation points.
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Affiliation(s)
- Elodie Laine
- Unité de Bioinformatique Structurale, CNRS URA 2185, Département de Biologie, Structurale et Chimie, Institut Pasteur, Paris, France
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31
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Zhang Y, Tan H, Jia Z, Chen G. Ligand-induced dimer formation of calmodulin. J Mol Recognit 2008; 21:267-74. [PMID: 18461636 DOI: 10.1002/jmr.895] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Calmodulin (CaM) can bind to numerous proteins in several interaction modes. Recently a new mode of interaction was discovered, in which two CaM molecules form an X-shaped dimer and two binding sites to trap the CaM-binding domain (CBD) of calcineurin subunit A. However, the X-shaped CaM dimer alone without ligand has not been observed. We performed molecular dynamics (MD) simulations and used MM_PBSA approach to investigate the properties of this new binding mode using ligand-bound and -free dimer systems. MD trajectories show that two peptides of CBD play a critical role in stabilizing the X-shaped conformation of the CaM dimer which would otherwise be unstable, leading to dimer disassembly in the absence of the ligands. Furthermore, we have analyzed the interaction free energy of the complex by MM-PBSA method and provide further evidence to demonstrate that the CBD peptide ligands are responsible for the stabilization of the dimer. Comparing this new binding mode with the classical one represented by CaM in complex with smooth muscle myosin light chain kinase, we conclude that this new binding mode is induced by the CBD of calcineurin subunit A. Our results explain the fact that the X-shaped CaM dimer structure has never been observed in the absence of ligands.
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Affiliation(s)
- Yong Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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32
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Houndonougbo Y, Kuczera K, Jas GS. Effects of CMAP and Electrostatic Cutoffs on the Dynamics of an Integral Membrane Protein: The Phospholamban Study. J Biomol Struct Dyn 2008; 26:17-34. [DOI: 10.1080/07391102.2008.10507220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Hu C, Fang J, Borchardt RT, Schowen RL, Kuczera K. Molecular dynamics simulations of domain motions of substrate-free S-adenosyl- L-homocysteine hydrolase in solution. Proteins 2008; 71:131-43. [PMID: 17932938 DOI: 10.1002/prot.21664] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
S-Adenosyl-L-homocysteine hydrolase (SAHH) is an enzyme regulating intracellular methylation reactions. The homotetrameric SAHH exists in an open conformation in absence of substrate, while enzyme:inhibitor complexes crystallize in the closed conformation, in which the ligands are engulfed by the protein due to an 18 degrees domain reorientation within each of the four subunits. We present a microscopic description of the structure and dynamics of the substrate-free, NAD(+)-bound SAHH in solution, based on a 15-ns molecular dynamics simulation in explicit solvent. In the trajectory, the four cofactor-binding domains formed a relatively rigid core with structure very similar to the crystal conformation. The four substrate-binding domains, located at the protein exterior, also retained internal structures similar to the crystal, while undergoing large amplitude rigid-body reorientations. The trajectory domain motions exhibited two interesting properties. First, within each subunit the domains fluctuated between open and closed conformations, while at the tetramer level 80% of the domain motions were perpendicular to the direction of the open-to-closed structural transition. Second, the domain reorientations in solution could be represented as a sum of two components, faster, with 20-50 ps correlation time and 3-4 degrees amplitude, and slower, with 8-23 ns correlation time and amplitude of 14-22 degrees . The faster motion is similar to the 1.5 cm(-1) frequency hinge-bending vibrations found in our recent normal mode analysis (Wang et al., Biochemistry 2005;44:7228-7239). The slower motion agrees with fluorescence anisotropy decay measurements, which detected a 10-20 ns domain reorientation of ca. 26 degrees amplitude in the substrate-free enzyme (Wang et al., Biochemistry 2006;45:7778-7786). Our simulations are thus in excellent agreement with experimental data. The simulations allow us to assign the observed nanosecond fluorescence anisotropy signal to fluctuations in domain orientations, and indicate that the microscopic mechanism of the motion involves rotational diffusion within a cone of 10-20 degrees . Overall, our simulation results complement the existing experimental data and provide important new insights into SAHH domain motions in solution, which play a crucial role in the catalytic mechanism of SAHH.
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Affiliation(s)
- Chen Hu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, USA
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34
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Zhang Y, Tan H, Lu Y, Jia Z, Chen G. Ca2+dissociation from the C-terminal EF-hand pair in calmodulin: A steered molecular dynamics study. FEBS Lett 2008; 582:1355-61. [DOI: 10.1016/j.febslet.2008.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 02/25/2008] [Accepted: 03/10/2008] [Indexed: 02/03/2023]
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35
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Laine E, Yoneda JD, Blondel A, Malliavin TE. The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis. Proteins 2008; 71:1813-29. [DOI: 10.1002/prot.21862] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Sinha N, Li Y, Lipschultz CA, Smith-Gill SJ. Understanding antibody–antigen associations by molecular dynamics simulations: Detection of important intra- and inter-molecular salt bridges. Cell Biochem Biophys 2007; 47:361-75. [PMID: 17652781 DOI: 10.1007/s12013-007-0031-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/28/2022]
Abstract
1 NSec molecular dynamics (MD) simulation of anti-hen egg white antibody, HyHEL63 (HH63), complexed with HEL reveals important molecular interactions, not revealed in its X-ray crystal structure. These molecular interactions were predicted to be critical for the complex formation, based on structure-function studies of this complex and 3-other anti-HEL antibodies, HH8, HH10 and HH26, HEL complexes. All four antibodies belong to the same structural family, referred to here as HH10 family. Ala scanning results show that they recognize 'coincident epitopes'. 1 NSec explicit, with periodic boundary condition, MD simulation of HH63- HEL reveals the presence of functionally important saltbridges. Around 200 ps in vacuo and an additional 20 ps explicit simulation agree with the observations from 1 Nsec simulation. Intra-molecular salt-bridges predicted to play significant roles in the complex formation, were revealed during MD simulation. A very stabilizing saltbridge network, and another intra-molecular salt-bridge, at the binding site of HEL, revealed during the MD simulation, is proposed to predipose binding site geometry for specific binding. All the revealed saltbridges are present in one or more of the other three complexes and/or involve \"hot-spot\" epitope and paratope residues. Most of these charged epitope residues make large contribution to the binding free energy. The "hot spot" epitope residue Lys97Y, which significantly contributes to the free energy of binding in all the complexes, forms an intermolecular salt-bridge in several MD conformers. Our earlier computations have shown that this inter-molecular salt-bridge plays a significant role in determining specificity and flexibility of binding in the HH8-HEL and HH26-HEL complexes. Using a robust criterion of salt-bridge detection, this intermolecular salt-bridge was detected in the native structures of the HH8-HEL and HH26-HEL complexes, but was not revealed in the crystal structure of HH63-HEL complex. The electrostatic strength of this revealed saltbridge was very strong. During 1 Nsec MD simulation this salt-bridge networks with another inter-molecular salt-bridge to form an inter-molecular salt-bridge triad. Participation of Lys97Y in the formation of inter-molecular triad further validates the functional importance of Lys97Y in HH63-HEL associations. These results demonstrate that many important structural details of biomolecular interactions can be better understood when studied in a dynamic environment, and that MD simulations can complement and expand information obtained from static X-ray structure. This study also highlights "hot-spot" molecular interactions in HyHEL63-HEL complex.
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Affiliation(s)
- Neeti Sinha
- Structural Biophysics Laboratory, Division of Basic Sciences, Bldg. 469 Frederick Cancer Research and Development Center, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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37
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Isvoran A, Craescu CT, Alexov E. Electrostatic control of the overall shape of calmodulin: numerical calculations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:225-37. [PMID: 17285296 DOI: 10.1007/s00249-006-0123-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 11/20/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
The paper reports the results of numerical calculations of the pKa's of the ionizable groups and the electrostatic interactions between calmodulin lobes in three different states of calmodulin: calcium-free, peptide-free; calcium-loaded, peptide-free; and calcium-loaded, peptide-bound. NMR and X-ray studies revealed that in these states the overall structure of calmodulin adopts various conformations referred as: disordered semi-compact, extended and compact conformations, respectively. In addition, a new X-ray structure was recently reported (Structure, 2003, 11, 1303) showing that calcium-loaded, peptide-free calmodulin can also adopt a compact conformation in addition to the well known extended conformation. The calculated energy changes of calcium-loaded, peptide-free calmodulin along the pathway connecting these two conformations provide a possible explanation for this structural plasticity. The effect of pH and organic compounds in the solution phase on the preference of calmodulin to adopt compact or extended conformations may be thus rationalized. Analysis of the contribution of the ionization changes to the energy of association of calmodulin lobes suggested that the formation of the compact forms requires protonation of several acidic residues. However, two different protonation scenarios are revealed: a protonation due to internal lobe organization and thus independent of the lobes association, and a protonation induced by the lobes association resulting to a proton uptake. In addition, the role of the individual residues on the energy of association of calmodulin lobes is calculated in two compact conformations (peptide-free and peptide-bound) and is shown that a set of residues always plays a dominant role in inter-domain interactions.
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Affiliation(s)
- A Isvoran
- Department of Chemistry, West University of Timisoara, Pestallozi 16, 300115 Timisoara, Romania
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38
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Settimo L, Donnini S, Juffer AH, Woody RW, Marin O. Conformational changes upon calcium binding and phosphorylation in a synthetic fragment of calmodulin. Biopolymers 2007; 88:373-85. [PMID: 17173306 DOI: 10.1002/bip.20657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have recently investigated by far-UV circular dichroism (CD) the effects of Ca(2+) binding and the phosphorylation of Ser 81 for the synthetic peptide CaM [54-106] encompassing the Ca(2+)-binding loops II and III and the central alpha helix of calmodulin (CaM) (Arrigoni et al., Biochemistry 2004, 43, 12788-12798). Using computational methods, we studied the changes in the secondary structure implied by these spectra with the aim to investigate the effect of Ca(2+) binding and the functional role of the phosphorylation of Ser 81 in the action of the full-length CaM. Ca(2+) binding induces the nucleation of helical structure by inducing side chain stacking of hydrophobic residues. We further investigated the effect of Ca(2+) binding by using near-UV CD spectroscopy. Molecular dynamics simulations of different fragments containing the central alpha-helix of CaM using various experimentally determined structures of CaM with bound Ca(2+) disclose the structural effects provided by the phosphorylation of Ser 81. This post-translational modification is predicted to alter the secondary structure in its surrounding and also to hinder the physiological bending of the central helix of CaM through an alteration of the hydrogen bond network established by the side chain of residue 81. Using quantum mechanical methods to predict the CD spectra for the frames obtained during the MD simulations, we are able to reproduce the relative experimental intensities in the far-UV CD spectra for our peptides. Similar conformational changes that take place in CaM [54-106] upon Ca(2+) binding and phosphorylation may occur in the full-length CaM.
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Affiliation(s)
- Luca Settimo
- CRIBI Biotechnology Centre, University of Padova, via U.Bassi, 58/b, 35131 Padova, Italy.
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39
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Ganoth A, Nachliel E, Friedman R, Gutman M. Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide. Proteins 2006; 64:133-46. [PMID: 16568447 DOI: 10.1002/prot.20956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Calmodulin (CaM) is a small (16.7 kDa), highly acidic protein that is crucial to all eukaryotes by serving as a prototypical calcium sensor. In the present study, we investigated, through molecular dynamics simulations, the dynamics of a complex between the Mlc1p protein, which is a CaM-like protein, and the IQ4 peptide. This protein-peptide interaction is of high importance because IQ motifs are widely distributed among different kinds of CaM-binding proteins. The Mlc1p-IQ4 complex, which had been resolved by crystallography to 2.1 A, confers to a Ca(+2)-independent stable structure. During the simulations, the complex undergoes a complicated modulation process, which involves bending of the angles between the alpha-helices of the protein, breaking of the alpha-helical structure of the IQ4 peptide into two sections, and formation of new contact points between the protein and the peptide. The dynamics of the process consist of fast sub picosecond events and much slower ones that take a few nanoseconds to completion. Our study expands the information embedded in the crystal structure of the Mlc1p-IQ4 complex by describing its dynamic behavior as it evolves from the crystal structure to a form stable in solution. The article shows that careful application of molecular dynamics simulations can be used for extending the structural information presented by the crystal structure, thereby revealing the dynamic configuration of the protein in its physiological environment.
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Affiliation(s)
- Assaf Ganoth
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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40
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Fiorin G, Pastore A, Carloni P, Parrinello M. Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail. Biophys J 2006; 91:2768-77. [PMID: 16877506 PMCID: PMC1578468 DOI: 10.1529/biophysj.106.086611] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of calcium-bound calmodulin (CaM) to recognize most of its target peptides is caused by its binding to two hydrophobic residues ('anchors'). In most of the CaM complexes, the anchors pack against the hydrophobic pockets of the CaM domains and are surrounded by fully conserved Met side chains. Here, by using metadynamics simulations, we investigate quantitatively the energetics of the final step of this process using the M13 peptide, which has a high affinity and spans the sequence of the skeletal myosin light chain kinase, an important natural CaM target. We established the accuracy of our calculations by a comparison between calculated and NMR-derived structural and dynamical properties. Our calculations provide novel insights into the mechanism of protein/peptide recognition: we show that the process is associated with a free energy gain similar to that experimentally measured for the CaM complex with the homologous smooth muscle MLCK peptide (Ehrhardt et al., 1995, Biochemistry 34, 2731). We suggest that binding is dominated by the entropic effect, in agreement with previous proposals. Furthermore, we explain the role of conserved methionines by showing that the large flexibility of these side chains is a key feature of the binding mechanism. Finally, we provide a rationale for the experimental observation that in all CaM complexes the C-terminal domain seems to be hierarchically more important in establishing the interaction.
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Affiliation(s)
- G Fiorin
- International School for Advanced Studies and Democritos Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
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41
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Ganoth A, Friedman R, Nachliel E, Gutman M. A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides. Biophys J 2006; 91:2436-50. [PMID: 16844751 PMCID: PMC1562369 DOI: 10.1529/biophysj.106.085399] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mlc1p protein from the budding yeast Saccharomyces cerevisiae is a Calmodulin-like protein, which interacts with IQ-motif peptides located at the yeast's myosin neck. In this study, we report a molecular dynamics study of the Mlc1p-IQ2 protein-peptide complex, starting with its crystal structure, and investigate its dynamics in an aqueous solution. The results are compared with those obtained by a previous study, where we followed the solution structure of the Mlc1p-IQ4 protein-peptide complex by molecular dynamics simulations. After the simulations, we performed an interaction free-energy analysis using the molecular mechanics Poisson-Boltzmann surface area approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the light-chain-binding domain of myosin V from the yeast S. cerevisiae is discussed.
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Affiliation(s)
- Assaf Ganoth
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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42
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Li H, Aluko RE. Structural modulation of calmodulin and calmodulin-dependent protein kinase II by pea protein hydrolysates. Int J Food Sci Nutr 2006; 57:178-89. [PMID: 17127468 DOI: 10.1080/09637480600659144] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The effects of two fractions of pea protein hydrolysate with high levels of positively charged amino acids on the structural conformations of calmodulin (CaM) and CaM-dependent protein kinase II (CaMKII) were determined using fluorescence and circular dichroism methods. In the presence of Ca2 + , addition of the protein hydrolysates to CaM and CaM/CaMKII complex led to increased exposure of aromatic groups as measured by intrinsic and extrinsic fluorescence spectroscopy. Near-UV circular dichroism data revealed an increase in the tertiary structure of CaM in the presence of pea protein hydrolysates. Effect of the protein hydrolysates on the CaM structure was greater with the fraction that contained higher contents of arginine and lysine when compared with the fraction with lower levels of these two amino acids. We concluded that the presence of the pea protein hydrolysates led to rearrangement of the native protein structure and exposure of buried hydrophobic groups of CaM and/or CaMKII.
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Affiliation(s)
- Huan Li
- Department of Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Chen Y, Zhang YZ, Zhou ZG, Wang G, Yi ZN. Identification of differently expressed genes in human colorectal adenocarcinoma. World J Gastroenterol 2006; 12:1025-32. [PMID: 16534841 PMCID: PMC4087892 DOI: 10.3748/wjg.v12.i7.1025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the differently expressed genes in human colorectal adenocarcinoma.
METHODS: The integrated approach for gene expression profiling that couples suppression subtractive hybridization, high-throughput cDNA array, sequencing, bioinformatics analysis, and reverse transcriptase real-time quantitative polymerase chain reaction (PCR) was carried out. A set of cDNA clones including 1260 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with florescent-labeled probes prepared from RNA of human colorectal adenocarcinoma (HCRAC) and normal colorectal tissues.
RESULTS: A total of 86 genes were identified, 16 unknown genes and 70 known genes. The transcription factor Sox9 influencing cell differentiation was downregulated. At the same time, Heat shock protein 10 KDis downregulated and Calmoulin is up-regulated.
CONCLUSION: Downregulation of heat shock protein 10 KD lost its inhibition of Ras, and then attenuated the Ras GTPase signaling pathway, increased cell proliferation and inhibited cell apoptosis. Down-regulated transcription factor So x 9 influences cell differentiation and cell-specific gene expression. Down-regulated So x 9 also decreases its binding to calmodulin, accumulates calmodulin as receptor-activated kinase and phosphorylase kinase due to the activation of PhK.
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Affiliation(s)
- Yao Chen
- Department of Anatomy, Basic and Legal Medical Institute, West China Medical Center, Sichuan University, Chengdu 610041, Sichuan Province, China.
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Polverini E, Boggs JM, Bates IR, Harauz G, Cavatorta P. Electron paramagnetic resonance spectroscopy and molecular modelling of the interaction of myelin basic protein (MBP) with calmodulin (CaM)—diversity and conformational adaptability of MBP CaM-targets. J Struct Biol 2004; 148:353-69. [PMID: 15522783 DOI: 10.1016/j.jsb.2004.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 07/30/2004] [Indexed: 11/26/2022]
Abstract
The classic 18.5 kDa isoform of murine myelin basic protein (mMBP) has been shown to bind calmodulin (CaM) strongly and specifically in vitro. Here, we have used site-directed spin labelling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy to map more precisely the sites of interaction of recombinant mMBP (rmMBP) with CaM. On the basis of these and previous experimental data, and the predictions of CaM-binding motifs using the Calmodulin Target Database (), three main segments of MBP were suggested for the interaction. The first site is located at the C-terminus; the second one lies in the central portion of the protein and forms an amphipathic alpha-helix in reconstituted myelin-mimetic systems; the third is quite close to the N-terminus. The murine Golli-MBP isoform J37 has also been shown to bind CaM in vitro, and an interaction site was predicted in the N-terminal Golli-specific portion of the protein. From these four segments, we selected peptide fragments of 12-14 residues in length, chosen on the bases of their amphipathicity and CaM-target characteristics. We modelled each of these peptides as alpha-helices, and performed docking simulations to investigate their interactions with the CaM peptide-binding tunnel. Different yet almost equally favourable CaM-binding modes were found for each of them. The experimental SDSL/EPR and theoretical modelling results were in good agreement, and supported the conjecture that there are several plausible CaM-binding sites in MBP, that could be induced into an alpha-helical conformation by their interaction with CaM and account for strong immobilisation of spin-labeled residues in all three segments. Phosphorylation and deimination were also emulated and simulated for known sites of MBP post-translational modification. The results obtained confirmed the appropriate utilisation of simple residue substitutions to mimic the natural modifications, and demonstrated molecular mechanisms by which MBP-CaM interactions could be modulated in vivo.
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Affiliation(s)
- Eugenia Polverini
- Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica, Università di Parma, Parco Area delle Scienze 7/A, 43100 Parma, Italy.
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