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Denesyuk AI, Permyakov SE, Permyakov EA, Johnson MS, Denessiouk K, Uversky VN. Canonical structural-binding modes in the calmodulin-target protein complexes. J Biomol Struct Dyn 2023; 41:7582-7594. [PMID: 36106955 DOI: 10.1080/07391102.2022.2123391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Intracellular calcium sensor protein calmodulin (CaM) belongs to the large EF-hand protein superfamily. CaM shows a unique and not fully understood ability to bind to multiple targets, allows them to participate in a variety of regulatory processes. The protein has two approximately symmetrical globular domains (the N- and C-lobes). Analysis of the CaM-binding sites of target proteins showed that they have two hydrophobic 'anchor' amino acids separated by 10 to 17 residues. Consequently, several CaM-binding motifs: {1-10}, {1-11}, {1-13}, {1-14}, {1-16}, {1-17}, differing by the distance between the two anchor residues along the amino acid sequence, have been identified. Despite extensive structural information on the role of target-protein amino acid residues in the formation of complexes with CaM, much less is known about the role of amino acids from CaM contributing to these interactions. In this work, a quantitative analysis of the contact surfaces of CaM and target proteins has been carried out for 35 representative three-dimensional structures. It has been shown that, in addition to the two hydrophobic terminal residues of the target fragment, the interaction also involves residues that are 4 residues earlier in the sequence (binding mode {1-5}). It has also been found that the N- and C-lobes of CaM bind the {1-5} motif located at the ends of the target in a structurally identical manner. Methionine residues at positions 51 (corresponding to 124 in the C-lobe), 71 (144), and 72 (145) of the CaM amino acid sequence are key hydrophobic residues for this interaction. They are located at the N- and C-boundaries of the even EF-hand motifs. The hydrophobic core of CaM ('Ф-quatrefoil') consists of 10 amino acids in the N-lobe (and in the C-lobe): Phe16 (Phe89), Phe19 (Phe92), Ile27 (Ile100), Thr29 (Ala102), Leu32 (Leu105), Ile52 (Ile125), Val55 (Ala128), Ile63 (Val136), Phe65 (Tyr138), and Phe68 (Phe141) and do not intersect with the target-binding methionine residues. CaM belongs to the 'dynamic' group of EF-hand proteins, in which calcium and protein ligand binding causes only global conformational changes but does not alter the conservative 'black' and 'grey' clusters described in our earlier works (PLoS One. 2014; 9(10):e109287). The membership of CaM in the 'dynamic' group is determined by the triggering and protective methionine layer: Met51 (Met124), Met71 (Met144) and Met72 (Met145). HIGHLIGHTSInterchain interactions in the unique 35 CaM complex structures were analyzed.Methionine amino acids of the N- and C-lobes of CaM form triggering and protective layers.Interactions of the target terminal residues with these methionine layers are structurally identical.CaM belonging to the 'dynamic' group is determined by the triggering and protective methionine layer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Dürvanger Z, Harmat V. Structural Diversity in Calmodulin - Peptide Interactions. Curr Protein Pept Sci 2020; 20:1102-1111. [PMID: 31553290 DOI: 10.2174/1389203720666190925101937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/13/2019] [Accepted: 04/12/2019] [Indexed: 01/17/2023]
Abstract
Calmodulin (CaM) is a highly conserved eukaryotic Ca2+ sensor protein that is able to bind a large variety of target sequences without a defined consensus sequence. The recognition of this diverse target set allows CaM to take part in the regulation of several vital cell functions. To fully understand the structural basis of the regulation functions of CaM, the investigation of complexes of CaM and its targets is essential. In this minireview we give an outline of the different types of CaM - peptide complexes with 3D structure determined, also providing an overview of recently determined structures. We discuss factors defining the orientations of peptides within the complexes, as well as roles of anchoring residues. The emphasis is on complexes where multiple binding modes were found.
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Affiliation(s)
- Zsolt Dürvanger
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Protein Modelling Research Group, Budapest, Hungary
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Buss M, Geerds C, Patschkowski T, Niehaus K, Niemann HH. Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallogr F Struct Biol Commun 2018; 74:345-350. [PMID: 29870018 PMCID: PMC5987742 DOI: 10.1107/s2053230x18006933] [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: 02/27/2018] [Accepted: 05/06/2018] [Indexed: 03/27/2024] Open
Abstract
Flavin-dependent halogenases can be used as biocatalysts because they regioselectively halogenate their substrates under mild reaction conditions. New halogenases with novel substrate specificities will add to the toolbox of enzymes available to organic chemists. HalX, the product of the xcc-b100_4193 gene, is a putative flavin-dependent halogenase from Xanthomonas campestris. The enzyme was recombinantly expressed and crystallized in order to aid in identifying its hitherto unknown substrate. Native data collected to a resolution of 2.5 Å showed indications of merohedral twinning in a hexagonal lattice. Attempts to solve the phase problem by molecular replacement failed. Here, a detailed analysis of the suspected twinning is presented. It is most likely that the crystals are trigonal (point group 3) and exhibit perfect hemihedral twinning so that they appear to be hexagonal (point group 6). As there are several molecules in the asymmetric unit, noncrystallographic symmetry may complicate twinning analysis and structure determination.
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Affiliation(s)
- Maren Buss
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Christina Geerds
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Thomas Patschkowski
- Faculty of Biology, Proteome and Metabolome Research, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Centre of Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Faculty of Biology, Proteome and Metabolome Research, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Centre of Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Hartmut H. Niemann
- Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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Westerlund AM, Delemotte L. Effect of Ca2+ on the promiscuous target-protein binding of calmodulin. PLoS Comput Biol 2018; 14:e1006072. [PMID: 29614072 PMCID: PMC5898786 DOI: 10.1371/journal.pcbi.1006072] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/13/2018] [Accepted: 03/07/2018] [Indexed: 01/05/2023] Open
Abstract
Calmodulin (CaM) is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.
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Affiliation(s)
- Annie M. Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail:
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Abbasi WA, Asif A, Andleeb S, Minhas FUAA. CaMELS:In silicoprediction of calmodulin binding proteins and their binding sites. Proteins 2017; 85:1724-1740. [DOI: 10.1002/prot.25330] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/13/2017] [Accepted: 06/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Wajid Arshad Abbasi
- Biomedical Informatics Research Laboratory, Department of Computer and Information Sciences (DCIS); Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore; Islamabad Pakistan
| | - Amina Asif
- Biomedical Informatics Research Laboratory, Department of Computer and Information Sciences (DCIS); Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore; Islamabad Pakistan
| | - Saiqa Andleeb
- Biotechnology Laboratory, Department of Zoology; University of AJ&K; Muzaffarabad AK Pakistan
| | - Fayyaz ul Amir Afsar Minhas
- Biomedical Informatics Research Laboratory, Department of Computer and Information Sciences (DCIS); Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore; Islamabad Pakistan
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