1
|
Cudia D, Ahoulou EO, Ames JB. Chemical shift assignments of retinal guanylyl cyclase activating protein 5 (GCAP5) with a mutation (R22A) that abolishes dimerization and enhances cyclase activation. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:115-119. [PMID: 37129703 PMCID: PMC10232645 DOI: 10.1007/s12104-023-10129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Retinal membrane guanylyl cyclases (RetGCs) in vertebrate rod and cone photoreceptors are activated by a family of neuronal Ca2+ sensor proteins called guanylyl cyclase activating proteins (GCAP1-7). GCAP5 from zebrafish photoreceptors binds to RetGC and confers Ca2+/Fe2+-dependent regulation of RetGC enzymatic activity that promotes the recovery phase of visual phototransduction. We report NMR chemical shift assignments of GCAP5 with a R22A mutation (called GCAP5R22A) that abolishes protein dimerization and activates RetGC with 3-fold higher activity than that of wild type GCAP5 (BMRB No. 51,783).
Collapse
Affiliation(s)
- Diana Cudia
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Effibe O Ahoulou
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
2
|
Bej A, Ames JB. Chemical shift assignments of calmodulin bound to the GluN1 C0 domain (residues 841-865) of the NMDA receptor. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:61-65. [PMID: 36739573 PMCID: PMC10232624 DOI: 10.1007/s12104-023-10121-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 05/31/2023]
Abstract
Neuroplasticity and synaptic transmission in the brain are regulated by N-methyl-D-aspartate receptors (NMDARs) that consist of hetero-tetrameric combinations of the glycine-binding GluN1 and glutamate-binding GluN2 subunits. Calmodulin (CaM) binds to the cytosolic C0 domain of GluN1 (residues 841-865) that may play a role in the Ca2+-dependent inactivation (CDI) of NMDAR channel activity. Dysregulation of NMDARs are linked to various neurological disorders, including Alzheimer's disease, depression, stroke, epilepsy, and schizophrenia. Here, we report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the GluN1 C0 domain of the human NMDAR (BMRB no. 51715).
Collapse
Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
3
|
Salveson I, Ames JB. Chemical shift assignments of the C-terminal domain of CaBP1 bound to the IQ-motif of voltage-gated Ca 2+ channel (Ca V1.2). BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:385-390. [PMID: 36064846 PMCID: PMC9510106 DOI: 10.1007/s12104-022-10108-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The neuronal L-type voltage-gated Ca2+ channel (CaV1.2) interacts with Ca2+ binding protein 1 (CaBP1), that promotes Ca2+-induced channel activity. The binding of CaBP1 to the IQ-motif in CaV1.2 (residues 1644-1665) blocks the binding of calmodulin and prevents Ca2+-dependent inactivation of CaV1.2. This Ca2+-induced binding of CaBP1 to CaV1.2 is important for modulating neuronal synaptic plasticity, which may serve a role in learning and memory. Here we report NMR assignments of the C-terminal domain of CaBP1 (residues 99-167, called CaBP1C) that contains two Ca2+ bound at the third and fourth EF-hands (EF3 and EF4) and is bound to the CaV1.2 IQ-motif from CaV1.2 (BMRB accession no. 51518).
Collapse
Affiliation(s)
- Ian Salveson
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
| |
Collapse
|
4
|
Bej A, Ames JB. Chemical shift assignments of calmodulin under standard conditions at neutral pH. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:213-218. [PMID: 35460468 PMCID: PMC9510097 DOI: 10.1007/s12104-022-10082-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/30/2022] [Indexed: 05/10/2023]
Abstract
The Ca2+ sensor protein, calmodulin (CaM) is ubiquitously expressed in all cells where it binds to hundreds of different target proteins, including dozens of enzymes, receptors, ion channels and numerous Ca2+ transporters. The only published NMR chemical shift assignments for Ca2+-bound CaM (in the absence of a target) have been determined under acidic conditions: at pH 6.5/310 K (BMRB 6541) and pH 6.3/320 K (BMRB 547). However, some CaM/target complexes are not soluble under these conditions. Also, amide chemical shifts are very sensitive to pH and temperature, which can cause large baseline errors when using the existing chemical shift assignments of free CaM to calculate chemical shift perturbations caused by target binding at neutral pH and physiological temperature. We report complete NMR chemical shift assignments of Ca2+-saturated CaM under a set of standard conditions at neutral pH and 308 K that will enable more accurate chemical shift comparison between free CaM and CaM/target complexes (BMRB 51289).
Collapse
Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
5
|
Bej A, Ames JB. Chemical shift assignments of calmodulin bound to a C-terminal site (residues 1120-1147) in the β-subunit of a retinal cyclic nucleotide-gated channel (CNGB1). BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:337-341. [PMID: 35986879 PMCID: PMC9510104 DOI: 10.1007/s12104-022-10101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Retinal cyclic nucleotide-gated (CNG) channels consist of two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to two separate sites within the cytosolic region of CNGB1: CaM binding to an N-terminal site (human CNGB1 residues 565-587, called CaM1) decreases the open probability of CNG channels at elevated Ca2+ levels in dark-adapted photoreceptors, whereas CaM binding to a separate C-terminal site (CNGB1 residues 1120-1147, called CaM2) may increase channel open probability in light activated photoreceptors. We recently reported NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM1 site of CNGB1 (BMRB no. 51222). Here, we report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the C-terminal CaM2 site of CNGB1 (BMRB no. 51447).
Collapse
Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
6
|
The accuracy of protein structures in solution determined by AlphaFold and NMR. Structure 2022; 30:925-933.e2. [DOI: 10.1016/j.str.2022.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 02/05/2023]
|
7
|
Bej A, Ames JB. Chemical shift assignments of calmodulin bound to the β-subunit of a retinal cyclic nucleotide-gated channel (CNGB1). BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:147-151. [PMID: 35107779 PMCID: PMC9068646 DOI: 10.1007/s12104-022-10072-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/24/2022] [Indexed: 05/25/2023]
Abstract
Rod cyclic nucleotide-gated (CNG) channels are formed by two protein subunits (CNGA1 and CNGB1). Calmodulin (CaM) binds to the cytosolic regulatory domain of CNGB1 and decreases the open probability of CNGA1/CNGB1 channels. The CaM binding site within bovine CNGB1 (residues 679-702) binds tightly to Ca2+-bound CaM, which promotes Ca2+-induced inactivation of CNGA1/CNGB1 channels in retinal rods. We report complete NMR chemical shift assignments of Ca2+-saturated CaM bound to the CaM-binding domain of CNGB1 (BMRB no. 51222).
Collapse
Affiliation(s)
- Aritra Bej
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
8
|
Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
Collapse
Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| |
Collapse
|
9
|
Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
Collapse
Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
| |
Collapse
|
10
|
Dalaloyan A, Martorana A, Barak Y, Gataulin D, Reuveny E, Howe A, Elbaum M, Albeck S, Unger T, Frydman V, Abdelkader EH, Otting G, Goldfarb D. Tracking Conformational Changes in Calmodulin in vitro, in Cell Extract, and in Cells by Electron Paramagnetic Resonance Distance Measurements. Chemphyschem 2019; 20:1860-1868. [PMID: 31054266 DOI: 10.1002/cphc.201900341] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Indexed: 12/12/2022]
Abstract
It is an open question whether the conformations of proteins sampled in dilute solutions are the same as in the cellular environment. Here we address this question by double electron-electron resonance (DEER) distance measurements with Gd(III) spin labels to probe the conformations of calmodulin (CaM) in vitro, in cell extract, and in human HeLa cells. Using the CaM mutants N53C/T110C and T34C/T117C labeled with maleimide-DOTA-Gd(III) in the N- and C-terminal domains, we observed broad and varied interdomain distance distributions. The in vitro distance distributions of apo-CaM and holo-CaM in the presence and absence of the IQ target peptide can be described by combinations of closed, open, and collapsed conformations. In cell extract, apo- and holo-CaM bind to target proteins in a similar way as apo- and holo-CaM bind to IQ peptide in vitro. In HeLa cells, however, in the presence or absence of elevated in-cell Ca2+ levels CaM unexpectedly produced more open conformations and very broad distance distributions indicative of many different interactions with in-cell components. These results show-case the importance of in-cell analyses of protein structures.
Collapse
Affiliation(s)
| | | | | | | | | | - Andrew Howe
- Department of Chemical and Biological Physics
| | | | - Shira Albeck
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Elwy H Abdelkader
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | |
Collapse
|
11
|
Cudia D, Ames JB. Chemical shift assignments of retinal guanylyl cyclase activating protein 5 (GCAP5). BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:201-205. [PMID: 30706384 PMCID: PMC6440817 DOI: 10.1007/s12104-019-09877-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 01/28/2019] [Indexed: 05/20/2023]
Abstract
Retinal membrane guanylyl cyclase (RetGC) in photoreceptor rod and cone cells is regulated by a family of guanylyl cyclase activating proteins (GCAP1-7). GCAP5 is expressed in zebrafish photoreceptors and promotes Ca2+-dependent regulation of RetGC enzymatic activity that regulates visual phototransduction. We report NMR chemical shift assignments of the Ca2+-free activator form of GCAP5 (BMRB No. 27705).
Collapse
Affiliation(s)
- Diana Cudia
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - James B Ames
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
12
|
Salveson I, Anderson DE, Hell JW, Ames JB. Chemical shift assignments of a calmodulin intermediate with two Ca 2+ bound in complex with the IQ-motif of voltage-gated Ca 2+ channels (Ca V1.2). BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:233-237. [PMID: 30788773 PMCID: PMC6440834 DOI: 10.1007/s12104-019-09883-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
Calcium-dependent inactivation (CDI) of neuronal voltage-gated Ca2+ channels (CaV1.2) is important for synaptic plasticity, which is associated with learning and memory. The Ca2+-dependent binding of calmodulin (CaM) to CaV1.2 is essential for CDI. Here we report NMR assignments for a CaM mutant (D21A/D23A/D25A/E32Q/D57A/D59A/N61A/E68Q, called CaMEF12) that contains two Ca2+ bound at the third and fourth EF-hands (EF3 and EF4) and is bound to the IQ-motif (residues 1644-1665) from CaV1.2 (BMRB accession no. 27692).
Collapse
Affiliation(s)
- Ian Salveson
- Department of Chemistry, University of California, 95616, Davis, CA, USA
| | - David E Anderson
- Department of Chemistry, University of California, 95616, Davis, CA, USA
| | - Johannes W Hell
- Department of Pharmacology, University of California, 95616, Davis, CA, USA
| | - James B Ames
- Department of Chemistry, University of California, 95616, Davis, CA, USA.
| |
Collapse
|
13
|
Grant BMM, Marshall CB, Ikura M. Expression and Purification of Calmodulin for NMR and Other Biophysical Applications. Methods Mol Biol 2019; 1929:207-221. [PMID: 30710275 DOI: 10.1007/978-1-4939-9030-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Calmodulin (CaM) is a ubiquitous calcium-sensing protein that has one of the most highly conserved sequences among eukaryotes. CaM has been a useful tool for biologists studying calcium signaling for decades. In recent years, CaM has also been implicated in numerous cancer-associated pathways, and rare CaM mutations have been identified as a cause of human cardiac arrhythmias. Here, we present a collection of our most recent and effective protocols for the expression and purification of recombinant CaM from Escherichia coli, including various isotopic labeling schemes, primarily for nuclear magnetic resonance (NMR) spectroscopy and other biophysical applications.
Collapse
Affiliation(s)
- Benjamin M M Grant
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| |
Collapse
|
14
|
Cho LTY, Alexandrou AJ, Torella R, Knafels J, Hobbs J, Taylor T, Loucif A, Konopacka A, Bell S, Stevens EB, Pandit J, Horst R, Withka JM, Pryde DC, Liu S, Young GT. An Intracellular Allosteric Modulator Binding Pocket in SK2 Ion Channels Is Shared by Multiple Chemotypes. Structure 2018; 26:533-544.e3. [PMID: 29576321 DOI: 10.1016/j.str.2018.02.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/03/2017] [Accepted: 02/23/2018] [Indexed: 01/22/2023]
Abstract
Small conductance potassium (SK) ion channels define neuronal firing rates by conducting the after-hyperpolarization current. They are key targets in developing therapies where neuronal firing rates are dysfunctional, such as in epilepsy, Parkinson's, and amyotrophic lateral sclerosis (ALS). Here, we characterize a binding pocket situated at the intracellular interface of SK2 and calmodulin, which we show to be shared by multiple small-molecule chemotypes. Crystallization of this complex revealed that riluzole (approved for ALS) and an analog of the anti-ataxic agent (4-chloro-phenyl)-[2-(3,5-dimethyl-pyrazol-1-yl)-pyrimidin-4-yl]-amine (CyPPA) bind to and allosterically modulate via this site. Solution-state nuclear magnetic resonance demonstrates that riluzole, NS309, and CyPPA analogs bind at this bipartite pocket. We demonstrate, by patch-clamp electrophysiology, that both classes of ligand interact with overlapping but distinct residues within this pocket. These data define a clinically important site, laying the foundations for further studies of the mechanism of action of riluzole and related molecules.
Collapse
Affiliation(s)
- Lily T-Y Cho
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Aristos J Alexandrou
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Rubben Torella
- Pfizer Worldwide Medicinal Chemistry, Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - John Knafels
- Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA
| | - Jake Hobbs
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Toni Taylor
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Alex Loucif
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Agnieszka Konopacka
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Sigourney Bell
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Edward B Stevens
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Jay Pandit
- Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA
| | - Reto Horst
- Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA
| | - Jane M Withka
- Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA
| | - David C Pryde
- Pfizer Worldwide Medicinal Chemistry, Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK
| | - Shenping Liu
- Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA.
| | - Gareth T Young
- Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK.
| |
Collapse
|
15
|
Villalobo A, Ishida H, Vogel HJ, Berchtold MW. Calmodulin as a protein linker and a regulator of adaptor/scaffold proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:507-521. [PMID: 29247668 DOI: 10.1016/j.bbamcr.2017.12.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 01/29/2023]
Abstract
Calmodulin (CaM) is a universal regulator for a huge number of proteins in all eukaryotic cells. Best known is its function as a calcium-dependent modulator of the activity of enzymes, such as protein kinases and phosphatases, as well as other signaling proteins including membrane receptors, channels and structural proteins. However, less well known is the fact that CaM can also function as a Ca2+-dependent adaptor protein, either by bridging between different domains of the same protein or by linking two identical or different target proteins together. These activities are possible due to the fact that CaM contains two independently-folded Ca2+ binding lobes that are able to interact differentially and to some degree separately with targets proteins. In addition, CaM can interact with and regulates several proteins that function exclusively as adaptors. This review provides an overview over our present knowledge concerning the structural and functional aspects of the role of CaM as an adaptor protein and as a regulator of known adaptor/scaffold proteins.
Collapse
Affiliation(s)
- Antonio Villalobo
- Department of Cancer Biology, Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Arturo Duperier 4, E-28029 Madrid, Spain.
| | - Hiroaki Ishida
- Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W., Calgary, Alberta T2N 1N4, Canada
| | - Hans J Vogel
- Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W., Calgary, Alberta T2N 1N4, Canada.
| | - Martin W Berchtold
- Department of Biology, University of Copenhagen, 13 Universitetsparken, DK-2100 Copenhagen Ø, Denmark.
| |
Collapse
|
16
|
Minnes L, Shaw DJ, Cossins BP, Donaldson PM, Greetham GM, Towrie M, Parker AW, Baker MJ, Henry AJ, Taylor RJ, Hunt NT. Quantifying Secondary Structure Changes in Calmodulin Using 2D-IR Spectroscopy. Anal Chem 2017; 89:10898-10906. [DOI: 10.1021/acs.analchem.7b02610] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lucy Minnes
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| | | | | | - Paul M. Donaldson
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Matthew J. Baker
- WestCHEM,
Department of Pure and Applied Chemistry, Technology and Innovation
Centre, University of Strathclyde, 99 George Street, Glasgow, G1 1RD, United Kingdom
| | | | | | - Neil T. Hunt
- Department
of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, United Kingdom
| |
Collapse
|
17
|
Evidence of the presence of a calmodulin-sensitive plasma membrane Ca 2+-ATPase in Trypanosoma equiperdum. Mol Biochem Parasitol 2017; 213:1-11. [PMID: 28213174 DOI: 10.1016/j.molbiopara.2017.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 01/01/2023]
Abstract
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca2+ regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca2+ homeostasis. Therefore, the plasma membrane Ca2+-ATPase (PMCA) is considered as a potential drug target. This is the first study revealing the presence of a PMCA in T. equiperdum (TePMCA) showing that it is calmodulin (CaM) sensitive, revealed by ATPase activity, western-blot analysis and immuno-absorption assays. The cloning sequence for TePMCA encodes a 1080 amino acid protein which contains domains conserved in all PMCAs so far studied. Molecular modeling predicted that the protein has 10 transmembrane and three cytoplasmic loops which include the ATP-binding site, the phosphorylation domain and Ca2+ translocation site. Like all PMCAs reported in other trypanosomatids, TePMCA lacks a classic CaM binding domain. Nevertheless, this enzyme presents in the C-terminal tail a region of 28 amino acids (TeC28), which most likely adopts a helical conformation within a 1-18 CaM binding motif. Molecular docking between Trypanosoma cruzi CaM (TcCaM) and TeC28 shows a significant similarity with the CaM-C28PMCA4b reference structure (2kne). TcCaM-TeC28 shows an anti-parallel interaction, the peptide wrapped by CaM and the anchor buried in the hydrophobic pocket, structural characteristic described for similar complexes. Our results allows to conclude that T. equiperdum possess a CaM-sensitive PMCA, which presents a non-canonical CaM binding domain that host a 1-18 motif.
Collapse
|
18
|
The Plasma Membrane Calcium Pump (PMCA): Regulation of Cytosolic Ca2+, Genetic Diversities and Its Role in Sub-plasma Membrane Microdomains. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 981:3-21. [DOI: 10.1007/978-3-319-55858-5_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
|
19
|
Structure of an intermediate conformer of the spindle checkpoint protein Mad2. Proc Natl Acad Sci U S A 2015; 112:11252-7. [PMID: 26305957 DOI: 10.1073/pnas.1512197112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spindle checkpoint senses unattached kinetochores during prometaphase and inhibits the anaphase-promoting complex or cyclosome (APC/C), thus ensuring accurate chromosome segregation. The checkpoint protein mitotic arrest deficient 2 (Mad2) is an unusual protein with multiple folded states. Mad2 adopts the closed conformation (C-Mad2) in a Mad1-Mad2 core complex. In mitosis, kinetochore-bound Mad1-C-Mad2 recruits latent, open Mad2 (O-Mad2) from the cytosol and converts it to an intermediate conformer (I-Mad2), which can then bind and inhibit the APC/C activator cell division cycle 20 (Cdc20) as C-Mad2. Here, we report the crystal structure and NMR analysis of I-Mad2 bound to C-Mad2. Although I-Mad2 retains the O-Mad2 fold in crystal and in solution, its core structural elements undergo discernible rigid-body movements and more closely resemble C-Mad2. Residues exhibiting methyl chemical shift changes in I-Mad2 form a contiguous, interior network that connects its C-Mad2-binding site to the conformationally malleable C-terminal region. Mutations of residues at the I-Mad2-C-Mad2 interface hinder I-Mad2 formation and impede the structural transition of Mad2. Our study provides insight into the conformational activation of Mad2 and establishes the basis of allosteric communication between two distal sites in Mad2.
Collapse
|
20
|
Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Hydrophobic Pocket for the C15-E,anti Chromophore in the Photoproduct. Biochemistry 2015; 54:3772-83. [DOI: 10.1021/acs.biochem.5b00438] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| |
Collapse
|
21
|
Calabrese AN, Bowie JH, Pukala TL. Structural analysis of calmodulin binding by nNOS inhibitory amphibian peptides. Biochemistry 2014; 54:567-76. [PMID: 25436860 DOI: 10.1021/bi5004124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Calmodulin (CaM) is a ubiquitous protein in nature and plays a regulatory role in numerous biological processes, including the upregulation of nitric oxide (NO) synthesis in vivo. Several peptides that prevent NO production by interacting with CaM have been isolated in the cutaneous secretions of Australian amphibians, and are thought to serve as a defense mechanism against predators. In this work, we probe the mechanism by which three of these peptides, namely, caerin 1.8, dahlein 5.6, and a synthetic modification of citropin 1.1, interact with CaM to inhibit NO signaling. Isothermal titration calorimetry was used to determine thermodynamic parameters of the binding interactions and revealed that all the peptides bind to CaM in a similar fashion, with the peptide encapsulated between the two lobes of CaM. Ion mobility-mass spectrometry was used to investigate the changes in collision cross section that occur as a result of complexation, providing additional evidence for this binding mode. Finally, nuclear magnetic resonance spectroscopy was used to track chemical shift changes upon binding. The results obtained confirm that these complexes adopt canonical collapsed structures and demonstrate the strength of the interaction between the peptides and CaM. An understanding of these molecular recognition events provides insights into the underlying mechanism of the amphibian host-defense system.
Collapse
Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide , Adelaide, SA Australia 5005
| | | | | |
Collapse
|
22
|
Piai A, Hošek T, Gonnelli L, Zawadzka-Kazimierczuk A, Koźmiński W, Brutscher B, Bermel W, Pierattelli R, Felli IC. "CON-CON" assignment strategy for highly flexible intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:209-18. [PMID: 25326659 DOI: 10.1007/s10858-014-9867-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/10/2014] [Indexed: 05/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the implementation of a set of novel ¹H-detected 5D experiments, (HACA)CON(CACO)NCO(CA)HA, BT-(H)NCO(CAN)CONNH and BT-HN(COCAN)CONNH, optimized for the study of highly flexible IDPs that exploit the best resolved correlations, those involving the carbonyl and nitrogen nuclei of neighboring amino acids, to achieve sequence-specific resonance assignment. Together with the analogous recently proposed pulse schemes based on ¹³C detection, they form a complete set of experiments for sequence-specific assignment of highly flexible IDPs. Depending on the particular sample conditions (concentration, lifetime, pH, temperature, etc.), these experiments present certain advantages and disadvantages that will be discussed. Needless to say, that the availability of a variety of complementary experiments will be important for accurate determination of resonance frequencies in complex IDPs.
Collapse
Affiliation(s)
- Alessandro Piai
- CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Kursula P. The many structural faces of calmodulin: a multitasking molecular jackknife. Amino Acids 2014; 46:2295-304. [PMID: 25005783 DOI: 10.1007/s00726-014-1795-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/22/2014] [Indexed: 12/16/2022]
Abstract
Calmodulin (CaM) is a highly conserved protein and a crucial calcium sensor in eukaryotes. CaM is a regulator of hundreds of diverse target proteins. A wealth of studies has been carried out on the structure of CaM, both in the unliganded form and in complexes with target proteins and peptides. The outcome of these studies points toward a high propensity to attain various conformational states, depending on the binding partner. The purpose of this review is to provide examples of different conformations of CaM trapped in the crystal state. In addition, comparisons are made to corresponding studies in solution. The different CaM conformations in crystal structures are also compared based on the positions of the metal ions bound to their EF hands, in terms of distances, angles, and pseudo-torsion angles. Possible caveats and artifacts in CaM crystal structures are discussed, as well as the possibilities of trapping biologically relevant CaM conformations in the crystal state.
Collapse
Affiliation(s)
- Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland,
| |
Collapse
|
24
|
Mruk K, Farley BM, Ritacco AW, Kobertz WR. Calmodulation meta-analysis: predicting calmodulin binding via canonical motif clustering. J Gen Physiol 2014; 144:105-14. [PMID: 24935744 PMCID: PMC4076516 DOI: 10.1085/jgp.201311140] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/21/2014] [Indexed: 11/20/2022] Open
Abstract
The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator to this meta-analysis resulted in a tool that identifies potential CaM-binding domains within a given sequence. To allow users to search for CaM-binding motifs within a protein of interest, perform the meta-analysis, and then compare the results to target peptide-CaM structures deposited in the Protein Data Bank, we created a website and online database. The availability of these tools and analyses will facilitate the design of CaM-related studies of ion channels and membrane transport proteins.
Collapse
Affiliation(s)
- Karen Mruk
- Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and
| | - Brian M Farley
- Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and
| | - Alan W Ritacco
- Department of Scientific and Research Computing, University of Massachusetts Medical School, Worcester, MA 01605
| | - William R Kobertz
- Department of Biochemistry and Molecular Pharmacology and Programs in Chemical Biology and Neuroscience, and
| |
Collapse
|
25
|
Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts. J Mol Biol 2014; 426:1826-38. [PMID: 24530797 DOI: 10.1016/j.jmb.2014.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 01/18/2014] [Accepted: 02/04/2014] [Indexed: 12/22/2022]
Abstract
Many protein molecules are formed by two or more domains whose structures and dynamics are closely related to their biological functions. It is thus important to develop methods to determine the structural properties of these multidomain proteins. Here, we characterize the interdomain motions in the calcium-bound state of calmodulin (Ca(2+)-CaM) using NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations. We find that the conformational fluctuations of the interdomain linker, which are largely responsible for the overall interdomain motions of CaM, can be well described by exploiting the information provided by chemical shifts. We thus identify 10 residues in the interdomain linker region that change their conformations upon substrate binding. Five of these residues (Met76, Lys77, Thr79, Asp80 and Ser81) are highly flexible and cover the range of conformations observed in the substrate-bound state, while the remaining five (Arg74, Lys75, Asp78, Glu82 and Glu83) are much more rigid and do not populate conformations typical of the substrate-bound form. The ensemble of conformations representing the Ca(2+)-CaM state obtained in this study is in good agreement with residual dipolar coupling, paramagnetic resonance enhancement, small-angle X-ray scattering and fluorescence resonance energy transfer measurements, which were not used as restraints in the calculations. These results provide initial evidence that chemical shifts can be used to characterize the conformational fluctuations of multidomain proteins.
Collapse
|
26
|
Kursula P. Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix. ACTA ACUST UNITED AC 2013; 70:24-30. [PMID: 24419375 DOI: 10.1107/s1399004713024437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022]
Abstract
Calmodulin is one of the most well characterized proteins and a widely used model system for calcium binding and large-scale protein conformational changes. Its long central helix is usually cut in half when a target peptide is bound. Here, two new crystal structures of calmodulin are presented, in which conformations possibly representing the first steps of calmodulin conformational collapse have been trapped. The central helix in the two structures is bent in the middle, causing a significant movement of the N- and C-terminal lobes with respect to one another. In both of the bent structures, a nearby polar side chain is inserted into the helical groove, disrupting backbone hydrogen bonding. The structures give an insight into the details of the factors that may be involved in the distortion of the central helix upon ligand peptide binding.
Collapse
Affiliation(s)
- Petri Kursula
- Department of Biochemistry and Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
27
|
Structural characterization of the interaction of human lactoferrin with calmodulin. PLoS One 2012; 7:e51026. [PMID: 23236421 PMCID: PMC3516504 DOI: 10.1371/journal.pone.0051026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/29/2012] [Indexed: 12/21/2022] Open
Abstract
Lactoferrin (Lf) is an 80 kDa, iron (Fe3+)-binding immunoregulatory glycoprotein secreted into most exocrine fluids, found in high concentrations in colostrum and milk, and released from neutrophil secondary granules at sites of infection and inflammation. In a number of cell types, Lf is internalized through receptor-mediated endocytosis and targeted to the nucleus where it has been demonstrated to act as a transcriptional trans-activator. Here we characterize human Lf’s interaction with calmodulin (CaM), a ubiquitous, 17 kDa regulatory calcium (Ca2+)-binding protein localized in the cytoplasm and nucleus of activated cells. Due to the size of this intermolecular complex (∼100 kDa), TROSY-based NMR techniques were employed to structurally characterize Ca2+-CaM when bound to intact apo-Lf. Both CaM’s backbone amides and the ε-methyl group of key methionine residues were used as probes in chemical shift perturbation and cross-saturation experiments to define the binding interface of apo-Lf on Ca2+-CaM. Unlike the collapsed conformation through which Ca2+-CaM binds the CaM-binding domains of its classical targets, Ca2+-CaM assumes an extended structure when bound to apo-Lf. Apo-Lf appears to interact predominantly with the C-terminal lobe of Ca2+-CaM, enabling the N-terminal lobe to potentially bind another target. Our use of intact apo-Lf has made possible the identification of a secondary interaction interface, removed from CaM’s primary binding domain. Secondary interfaces play a key role in the target’s response to CaM binding, highlighting the importance of studying intact complexes. This solution-based approach can be applied to study other regulatory calcium-binding EF-hand proteins in intact intermolecular complexes.
Collapse
|
28
|
Stauch K, Kieken F, Sorgen P. Characterization of the structure and intermolecular interactions between the connexin 32 carboxyl-terminal domain and the protein partners synapse-associated protein 97 and calmodulin. J Biol Chem 2012; 287:27771-88. [PMID: 22718765 PMCID: PMC3431650 DOI: 10.1074/jbc.m112.382572] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/20/2012] [Indexed: 12/20/2022] Open
Abstract
In Schwann cells, connexin 32 (Cx32) can oligomerize to form intracellular gap junction channels facilitating a shorter pathway for metabolite diffusion across the layers of the myelin sheath. The mechanisms of Cx32 intracellular channel regulation have not been clearly defined. However, Ca(2+), pH, and the phosphorylation state can regulate Cx32 gap junction channels, in addition to the direct interaction of protein partners with the carboxyl-terminal (CT) domain. In this study, we used different biophysical methods to determine the structure and characterize the interaction of the Cx32CT domain with the protein partners synapse-associated protein 97 (SAP97) and calmodulin (CaM). Our results revealed that the Cx32CT is an intrinsically disordered protein that becomes α-helical upon binding CaM. We identified the GUK domain as the minimal SAP97 region necessary for the Cx32CT interaction. The Cx32CT residues affected by the binding of CaM and the SAP97 GUK domain were determined as well as the dissociation constants for these interactions. We characterized three Cx32CT Charcot-Marie-Tooth disease mutants (R219H, R230C, and F235C) and identified that whereas they all formed functional channels, they all showed reduced binding affinity for SAP97 and CaM. Additionally, we report that in RT4-D6P2T rat schwannoma cells, Cx32 is differentially phosphorylated and exists in a complex with SAP97 and CaM. Our studies support the importance of protein-protein interactions in the regulation of Cx32 gap junction channels and myelin homeostasis.
Collapse
Affiliation(s)
- Kelly Stauch
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Fabien Kieken
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Paul Sorgen
- From the Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198
| |
Collapse
|
29
|
Atilgan AR, Aykut AO, Atilgan C. Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J Chem Phys 2011; 135:155102. [DOI: 10.1063/1.3651807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
30
|
Schweimer K, Prasch S, Sujatha PS, Bubunenko M, Gottesman ME, Rösch P. NusA interaction with the α subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition. Structure 2011; 19:945-54. [PMID: 21742261 PMCID: PMC3134791 DOI: 10.1016/j.str.2011.03.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/28/2011] [Accepted: 03/05/2011] [Indexed: 10/18/2022]
Abstract
Elongating Escherichia coli RNAP is modulated by NusA protein. The C-terminal domain (CTD) of the RNAP α subunit (αCTD) interacts with the acidic CTD 2 (AR2) of NusA, releasing the autoinhibitory blockade of the NusA S1-KH1-KH2 motif and allowing NusA to bind nascent nut spacer RNA. We determined the solution conformation of the AR2:αCTD complex. The αCTD residues that interface with AR2 are identical to those that recognize UP promoter elements A nusA-ΔAR2 mutation does not affect UP-dependent rrnH transcription initiation in vivo. Instead, the mutation inhibits Rho-dependent transcription termination at phage λtR1, which lies adjacent to the λnutR sequence. The Rho-dependent λtimm terminator, which is not preceded by a λnut sequence, is fully functional. We propose that constitutive binding of NusA-ΔAR2 to λnutR occludes Rho. In addition, the mutation confers a dominant defect in exiting stationary phase.
Collapse
Affiliation(s)
- Kristian Schweimer
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Stefan Prasch
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Pagadala Santhanam Sujatha
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Mikhail Bubunenko
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
- Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Max E. Gottesman
- Department of Microbiology and Immunology and Institute of Cancer Research, Columbia University Medical Center, New York, New York 10032
| | - Paul Rösch
- Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| |
Collapse
|
31
|
Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH. A novel strategy for NMR resonance assignment and protein structure determination. JOURNAL OF BIOMOLECULAR NMR 2011; 49:27-38. [PMID: 21161328 PMCID: PMC3715383 DOI: 10.1007/s10858-010-9458-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/16/2010] [Indexed: 05/11/2023]
Abstract
The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution - especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.
Collapse
Affiliation(s)
- Alexander Lemak
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- The Northeast Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Aleksandras Gutmanas
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- The Northeast Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Seth Chitayat
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Murthy Karra
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Christophe Farès
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- The Northeast Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Maria Sunnerhagen
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Cheryl H. Arrowsmith
- Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
- The Northeast Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada,
| |
Collapse
|
32
|
Abstract
AbstractOptimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.
Collapse
|
33
|
Wyttenbach T, Grabenauer M, Thalassinos K, Scrivens JH, Bowers MT. The effect of calcium ions and peptide ligands on the relative stabilities of the calmodulin dumbbell and compact structures. J Phys Chem B 2010; 114:437-47. [PMID: 20000583 DOI: 10.1021/jp906242m] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Ca(n)(2+)-CaM complexes were observed in calcium-containing solutions, n = 0-4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n = 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII(290-309), the CaM target domain of the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca(4)(2+)-CaM-CaMKII(290-309) complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM-peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM-peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.
Collapse
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | | | | | | | | |
Collapse
|
34
|
Abi-Ghanem J, Heddi B, Foloppe N, Hartmann B. DNA structures from phosphate chemical shifts. Nucleic Acids Res 2010; 38:e18. [PMID: 19942687 PMCID: PMC2817473 DOI: 10.1093/nar/gkp1061] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 10/14/2009] [Accepted: 11/01/2009] [Indexed: 01/04/2023] Open
Abstract
For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the (31)P chemical shifts (deltaP) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate deltaP into distance restraints directly exploitable in structural refinement. It even provides a new method for refining DNA oligomers with restraints exclusively inferred from deltaP. Combined with molecular dynamics in explicit solvent, these restraints lead to a structural and dynamical view of the DNA as detailed as that obtained with conventional and more extensive restraints. Tests with the Jun-Fos oligomer show that this deltaP-based strategy can provide a simple and straightforward method to capture DNA properties in solution, from routine NMR experiments on unlabeled samples.
Collapse
Affiliation(s)
- Joséphine Abi-Ghanem
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brahim Heddi
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Nicolas Foloppe
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brigitte Hartmann
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| |
Collapse
|
35
|
Zhou Y, Yang W, Lurtz MM, Chen Y, Jiang J, Huang Y, Louis CF, Yang JJ. Calmodulin mediates the Ca2+-dependent regulation of Cx44 gap junctions. Biophys J 2009; 96:2832-48. [PMID: 19348766 DOI: 10.1016/j.bpj.2008.12.3941] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Revised: 12/07/2008] [Accepted: 12/23/2008] [Indexed: 10/20/2022] Open
Abstract
We have shown previously that the Ca2+-dependent inhibition of lens epithelial cell-to-cell communication is mediated in part by the direct association of calmodulin (CaM) with connexin43 (Cx43), the major connexin in these cells. We now show that elevation of [Ca2+](i) in HeLa cells transfected with the lens fiber cell gap junction protein sheep Cx44 also results in the inhibition of cell-to-cell dye transfer. A peptide comprising the putative CaM binding domain (aa 129-150) of the intracellular loop region of this connexin exhibited a high affinity, stoichiometric interaction with Ca2+-CaM. NMR studies indicate that the binding of Cx44 peptide to CaM reflects a classical embracing mode of interaction. The interaction is an exothermic event that is both enthalpically and entropically driven in which electrostatic interactions play an important role. The binding of the Cx44 peptide to CaM increases the CaM intradomain cooperativity and enhances the Ca2+-binding affinities of the C-domain of CaM more than twofold by slowing the rate of Ca2+ release from the complex. Our data suggest a common mechanism by which the Ca2+-dependent inhibition of the alpha-class of gap junction proteins is mediated by the direct association of an intracellular loop region of these proteins with Ca2+-CaM.
Collapse
Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Peña PV, Musselman CA, Kuo AJ, Gozani, Kutateladze TG. NMR assignments and histone specificity of the ING2 PHD finger. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:352-8. [PMID: 19184981 PMCID: PMC2758779 DOI: 10.1002/mrc.2390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The ING2 plant homeodomain (PHD) finger is recruited to the nucleosome through specific binding to histone H3 trimethylated at lysine 4 (H3K4me3). Here, we describe backbone and side chain assignments of the ING2 PHD finger, analyze its binding to the unmodified and modified histone and p53 peptides, and map the histone H3 and H3K4me3 binding sites based on chemical shift perturbation analysis.
Collapse
Affiliation(s)
- Pedro V. Peña
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Catherine A. Musselman
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Alex J. Kuo
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Gozani
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| |
Collapse
|
37
|
Libich DS, Harauz G. Solution NMR and CD spectroscopy of an intrinsically disordered, peripheral membrane protein: evaluation of aqueous and membrane-mimetic solvent conditions for studying the conformational adaptability of the 18.5 kDa isoform of myelin basic protein (MBP). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1015-29. [PMID: 18449534 DOI: 10.1007/s00249-008-0334-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 04/09/2008] [Accepted: 04/11/2008] [Indexed: 02/05/2023]
Abstract
The stability and secondary structure propensity of recombinant murine 18.5 kDa myelin basic protein (rmMBP, 176 residues) was assessed using circular dichroic and nuclear magnetic resonance spectroscopy (1H-15N HSQC experiments) to determine the optimal sample conditions for further NMR studies (i.e., resonance assignments and protein-protein interactions). Six solvent conditions were selected based on their ability to stabilise the protein, and their tractability to currently standard solution NMR methodology. Selected solvent conditions were further characterised as functions of concentration, temperature, and pH. The results of these trials indicated that 30% TFE-d2 in H2O (v/v), pH 6.5 at 300 K, and 100 mM KCl, pH 6.5 at 277 K were the best conditions to use for future solution NMR studies of MBP. Micelles of DPC were found to be inappropriate for backbone resonance assignments of rmMBP in this instance.
Collapse
Affiliation(s)
- David S Libich
- Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, ON, Canada
| | | |
Collapse
|
38
|
Backbone dynamics of the 18.5 kDa isoform of myelin basic protein reveals transient alpha-helices and a calmodulin-binding site. Biophys J 2008; 94:4847-66. [PMID: 18326633 DOI: 10.1529/biophysj.107.125823] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The 18.5 kDa isoform of myelin basic protein (MBP) is the predominant form in adult human central nervous system myelin. It is an intrinsically disordered protein that functions both in membrane adhesion, and as a linker connecting the oligodendrocyte membrane to the underlying cytoskeleton; its specific interactions with calmodulin and SH3-domain containing proteins suggest further multifunctionality in signaling. Here, we have used multidimensional heteronuclear nuclear magnetic resonance spectroscopy to study the conformational dependence on environment of the protein in aqueous solution (100 mM KCl) and in a membrane-mimetic solvent (30% TFE-d(2)), particularly to analyze its secondary structure using chemical shift indexing, and to investigate its backbone dynamics using (15)N spin relaxation measurements. Collectively, the data revealed three major segments of the protein with a propensity toward alpha-helicity that was stabilized by membrane-mimetic conditions: T33-D46, V83-T92, and T142-L154 (murine 18.5 kDa sequence numbering). All of these regions corresponded with bioinformatics predictions of ordered secondary structure. The V83-T92 region comprises a primary immunodominant epitope that had previously been shown by site-directed spin labeling and electron paramagnetic resonance spectroscopy to be alpha-helical in membrane-reconstituted systems. The T142-L154 segment overlapped with a predicted calmodulin-binding site. Chemical shift perturbation experiments using labeled MBP and unlabeled calmodulin demonstrated a dramatic conformational change in MBP upon association of the two proteins, and were consistent with the C-terminal segment of MBP being the primary binding site for calmodulin.
Collapse
|
39
|
Zhou Y, Yang W, Lurtz MM, Ye Y, Huang Y, Lee HW, Chen Y, Louis CF, Yang JJ. Identification of the Calmodulin Binding Domain of Connexin 43. J Biol Chem 2007; 282:35005-17. [PMID: 17901047 DOI: 10.1074/jbc.m707728200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calmodulin (CaM) has been implicated in mediating the Ca(2+)-dependent regulation of gap junctions. This report identifies a CaM-binding motif comprising residues 136-158 in the intracellular loop of Cx43. A 23-mer peptide encompassing this CaM-binding motif was shown to bind Ca(2+)-CaM with 1:1 stoichiometry by using various biophysical approaches, including surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and NMR. Far UV circular dichroism studies indicated that the Cx43-derived peptide increased its alpha-helical contents on CaM binding. Fluorescence and NMR studies revealed conformational changes of both the peptide and CaM following formation of the CaM-peptide complex. The apparent dissociation constant of the peptide binding to CaM in physiologic K(+) is in the range of 0.7-1 microM. Upon binding of the peptide to CaM, the apparent K(d) of Ca(2+) for CaM decreased from 2.9 +/- 0.1 to 1.6 +/- 0.1 microM, and the Hill coefficient n(H) increased from 2.1 +/- 0.1 to 3.3 +/- 0.5. Transient expression in HeLa cells of two different mutant Cx43-EYFP constructs without the putative Cx43 CaM-binding site eliminated the Ca(2+)-dependent inhibition of Cx43 gap junction permeability, confirming that residues 136-158 in the intracellular loop of Cx43 contain the CaM-binding site that mediates the Ca(2+)-dependent regulation of Cx43 gap junctions. Our results provide the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx43 in a Ca(2+)-dependent manner, providing a molecular basis for the well characterized Ca(2+)-dependent inhibition of Cx43-containing gap junctions.
Collapse
Affiliation(s)
- Yubin Zhou
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Rainaldi M, Yamniuk AP, Murase T, Vogel HJ. Calcium-dependent and -independent binding of soybean calmodulin isoforms to the calmodulin binding domain of tobacco MAPK phosphatase-1. J Biol Chem 2007; 282:6031-42. [PMID: 17202149 DOI: 10.1074/jbc.m608970200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The recent finding of an interaction between calmodulin (CaM) and the tobacco mitogen-activated protein kinase phosphatase-1 (NtMKP1) establishes an important connection between Ca(2+) signaling and the MAPK cascade, two of the most important signaling pathways in plant cells. Here we have used different biophysical techniques, including fluorescence and NMR spectroscopy as well as microcalorimetry, to characterize the binding of soybean CaM isoforms, SCaM-1 and -4, to synthetic peptides derived from the CaM binding domain of NtMKP1. We find that the actual CaM binding region is shorter than what had previously been suggested. Moreover, the peptide binds to the SCaM C-terminal domain even in the absence of free Ca(2+) with the single Trp residue of the NtMKP1 peptides buried in a solvent-inaccessible hydrophobic region. In the presence of Ca(2+), the peptides bind first to the C-terminal lobe of the SCaMs with a nanomolar affinity, and at higher peptide concentrations, a second peptide binds to the N-terminal domain with lower affinity. Thermodynamic analysis demonstrates that the formation of the peptide-bound complex with the Ca(2+)-loaded SCaMs is driven by favorable binding enthalpy due to a combination of hydrophobic and electrostatic interactions. Experiments with CaM proteolytic fragments showed that the two domains bind the peptide in an independent manner. To our knowledge, this is the first report providing direct evidence for sequential binding of two identical peptides of a target protein to CaM. Discussion of the potential biological role of this interaction motif is also provided.
Collapse
Affiliation(s)
- Mario Rainaldi
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | | | | | | |
Collapse
|
41
|
Novak P, Havlicek V, Derrick PJ, Beran KA, Bashir S, Giannakopulos AE. Monitoring conformational changes in protein complexes using chemical cross-linking and Fourier transform ion cyclotron resonance mass spectrometry: the effect of calcium binding on the calmodulin-melittin complex. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2007; 13:281-290. [PMID: 17942978 DOI: 10.1255/ejms.882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Calmodulin is an EF hand calcium binding protein. Its binding affinities to various protein/peptide targets often depend on the conformational changes induced by the binding of calcium. One such target is melittin, which binds tightly to calmodulin in the presence of calcium, and inhibits its function. Chemical cross-linking combined with Fourier transform ion cyclotron resonance mass spectrometry has been employed to investigate the coordination of calmodulin and melittin in the complex at different concentrations of calcium. This methodology can be used to monitor structural changes of proteins induced by ligand binding, and study the effects these changes have on non- covalent interactions between proteins. Cross-linking results indicate that the binding place of the first melittin in the calcium free calmodulin form is the same as in the calcium loaded calmodulin/melittin complex.
Collapse
Affiliation(s)
- Petr Novak
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | | | | | | | | |
Collapse
|
42
|
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.
Collapse
Affiliation(s)
- Luca Settimo
- CRIBI Biotechnology Centre, University of Padova, via U.Bassi, 58/b, 35131 Padova, Italy.
| | | | | | | | | |
Collapse
|
43
|
Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Mei Ono A, Güntert P. Optimal isotope labelling for NMR protein structure determinations. Nature 2006; 440:52-7. [PMID: 16511487 DOI: 10.1038/nature04525] [Citation(s) in RCA: 357] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 12/14/2005] [Indexed: 11/09/2022]
Abstract
Nuclear-magnetic-resonance spectroscopy can determine the three-dimensional structure of proteins in solution. However, its potential has been limited by the difficulty of interpreting NMR spectra in the presence of broadened and overlapping resonance lines and low signal-to-noise ratios. Here we present stereo-array isotope labelling (SAIL), a technique that can overcome many of these problems by applying a complete stereospecific and regiospecific pattern of stable isotopes that is optimal with regard to the quality and information content of the resulting NMR spectra. SAIL uses exclusively chemically and enzymatically synthesized amino acids for cell-free protein expression. We demonstrate for the 17-kDa protein calmodulin and the 41-kDa maltodextrin-binding protein that SAIL offers sharpened lines, spectral simplification without loss of information, and the ability to rapidly collect the structural restraints required to solve a high-quality solution structure for proteins twice as large as commonly solved by NMR. It thus makes a large class of proteins newly accessible to detailed solution structure determination.
Collapse
Affiliation(s)
- Masatsune Kainosho
- CREST/JST and Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan.
| | | | | | | | | | | |
Collapse
|
44
|
Fiorin G, Biekofsky RR, Pastore A, Carloni P. Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study. Proteins 2005; 61:829-39. [PMID: 16193483 DOI: 10.1002/prot.20597] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The fold of calmodulin (CaM) consists of two globular domains connected by a helical segment (the linker), whose conformational properties play a crucial role for the protein's molecular recognition processes. Here we investigate the structural properties of the linker by performing a 11.5 ns molecular dynamics (MD) simulation of calcium-loaded human CaM in aqueous solution. The calculations are based on the AMBER force field. The calculated S2 order parameters are in good accord with NMR data: The structure of the linker in our simulations is much more flexible than that emerging from the Homo sapiens X-ray structure, consistently with the helix unwinding observed experimentally in solution. This process occurs spontaneously in a nanosecond timescale, as observed also in a very recent simulation based on the GROMOS force field. A detailed description of the mechanism that determines the linker unwinding is provided, in which electrostatic contacts between the two globular domains play a critical role. The orientation of the domains emerging from our MD calculations is consistent both with former X-ray scattering data and a recent NMR work. Based on our findings, a rationale for the experimentally measured entropy cost associated to binding to the protein's cellular partners is also given.
Collapse
Affiliation(s)
- G Fiorin
- SISSA-International School for Advanced Studies, INFM-Democritos Modeling Center for Research in Atomistic Simulation, Trieste, Italy
| | | | | | | |
Collapse
|
45
|
Larsson G, Schleucher J, Onions J, Hermann S, Grundström T, Wijmenga SS. Backbone dynamics of a symmetric calmodulin dimer in complex with the calmodulin-binding domain of the basic-helix-loop-helix transcription factor SEF2-1/E2-2: a highly dynamic complex. Biophys J 2005; 89:1214-26. [PMID: 15894636 PMCID: PMC1366606 DOI: 10.1529/biophysj.104.055780] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 05/04/2005] [Indexed: 11/18/2022] Open
Abstract
Calmodulin (CaM) interacts specifically as a dimer with some dimeric basic-Helix-Loop-Helix (bHLH) transcription factors via a novel high affinity binding mode. Here we report a study of the backbone dynamics by (15)N-spin relaxation on the CaM dimer in complex with a dimeric peptide that mimics the CaM binding region of the bHLH transcription factor SEF2-1. The relaxation data were measured at multiple magnetic fields, and analyzed in a model-free manner using in-house written software designed to detect nanosecond internal motion. Besides picosecond motions, all residues also experience internal motion with an effective correlation time of approximately 2.5 ns with squared order parameter (S(2)) of approximately 0.75. Hydrodynamic calculations suggest that this can be attributed to motions of the N- and C-terminal domains of the CaM dimer in the complex. Moreover, residues with significant exchange broadening are found. They are clustered in the CaM:SEF2-1mp binding interface, the CaM:CaM dimer interface, and in the flexible helix connecting the CaM N- and C-terminal domains, and have similar exchange times (approximately 50 micros), suggesting a cooperative mechanism probably caused by protein:protein interactions. The dynamic features presented here support the conclusion that the conformationally heterogeneous bHLH mimicking peptide trapped inside the CaM dimer exchanges between different binding sites on both nanosecond and microsecond timescales. Nature has thus found a way to specifically recognize a relatively ill-fitting target. This novel mode of target-specific binding, which neither belongs to lock-and-key nor induced-fit binding, is characterized by dimerization and continuous exchange between multiple flexible binding alternatives.
Collapse
Affiliation(s)
- Göran Larsson
- Department of Medical Biochemistry and Biophysics, University of Umeå, Sweden
| | | | | | | | | | | |
Collapse
|
46
|
Wong JWH, Maleknia SD, Downard KM. Hydroxyl radical probe of the calmodulin-melittin complex interface by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:225-233. [PMID: 15694772 DOI: 10.1016/j.jasms.2004.11.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 11/11/2004] [Accepted: 11/12/2004] [Indexed: 05/24/2023]
Abstract
The calcium-dependent interaction of calmodulin and melittin is studied through the application of a radical probe approach in which solutions of the protein and peptide and protein alone are subjected to high fluxes of hydroxyl and other oxygen radicals on millisecond timescales. These radicals are generated by an electrical discharge within an electrospray ion source of a mass spectrometer. Condensation of the electrosprayed droplets followed by proteolytic digestion of both calmodulin and melittin has identified residues in both which participate in the interaction and/or are shielded from solvent within the protein complex. Consistent with other theoretical models and available experimental data, the tryptophan residue of melittin at position 19 is shown to be critical to the formation of the complex with the C-terminal domain of peptide enveloped by and protected from oxidation upon binding to the protein. Furthermore, the N-terminal domain (to residue 36) and tyrosine at position 99 in calmodulin are significantly protected from limited oxidation upon the binding of melittin while exposing the phenylalanine residue at position 92 of the flexible loop domain. The N-terminus (through residue 36) of calmodulin is shown to lie in closer proximity to the melittin helix than its C-terminal counterpart (residues 127-148) based upon the protection levels measured at reactive residues within these segments of the protein.
Collapse
Affiliation(s)
- Jason W H Wong
- School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, Australia
| | | | | |
Collapse
|
47
|
Xiong L, Kleerekoper QK, He R, Putkey JA, Hamilton SL. Sites on Calmodulin That Interact with the C-terminal Tail of Cav1.2 Channel. J Biol Chem 2005; 280:7070-9. [PMID: 15583004 DOI: 10.1074/jbc.m410558200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two fragments of the C-terminal tail of the alpha(1) subunit (CT1, amino acids 1538-1692 and CT2, amino acids 1596-1692) of human cardiac L-type calcium channel (Ca(V)1.2) have been expressed, refolded, and purified. A single Ca(2+)-calmodulin binds to each fragment, and this interaction with Ca(2+)-calmodulin is required for proper folding of the fragment. Ca(2+)-calmodulin, bound to these fragments, is in a more extended conformation than calmodulin bound to a synthetic peptide representing the IQ motif, suggesting that either the conformation of the IQ sequence is different in the context of the longer fragment, or other sequences within CT2 contribute to the binding of calmodulin. NMR amide chemical shift perturbation mapping shows the backbone conformation of calmodulin is nearly identical when bound to CT1 and CT2, suggesting that amino acids 1538-1595 do not contribute to or alter calmodulin binding to amino acids 1596-1692 of Ca(V)1.2. The interaction with CT2 produces the greatest changes in the backbone amides of hydrophobic residues in the N-lobe and hydrophilic residues in the C-lobe of calmodulin and has a greater effect on residues located in Ca(2+) binding loops I and II in the N-lobe relative to loops III and IV in the C-lobe. In conclusion, Ca(2+)-calmodulin assumes a novel conformation when part of a complex with the C-terminal tail of the Ca(V)1.2 alpha(1) subunit that is not duplicated by synthetic peptides corresponding to the putative binding motifs.
Collapse
Affiliation(s)
- Liangwen Xiong
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | |
Collapse
|
48
|
Brokx RD, Scheek RM, Weljie AM, Vogel HJ. Backbone dynamic properties of the central linker region of calcium-calmodulin in 35% trifluoroethanol. J Struct Biol 2005; 146:272-80. [PMID: 15099569 DOI: 10.1016/j.jsb.2003.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 12/16/2003] [Indexed: 10/26/2022]
Abstract
The backbone dynamic properties of uniformly (15)N-labeled calcium-saturated calmodulin (Ca(2+)-CaM) in 35% 2,2,2-trifluoroethanol (TFE) have been examined by (15)N NMR relaxation methods. This particular solvent was chosen in order to mimic the conditions in which CaM was crystallized, which included the presence of alcohols. Special attention was paid to the central linker region of Ca(2+)-CaM, which is a long, solvent-exposed alpha-helix in the crystal structure but is known to be partially unwound and flexible in solution. (15)N T(1), T(2), and (15)N-[(1)H] NOE values were determined for both Ca(2+)-CaM in H(2)O and Ca(2+)-CaM in 35% TFE, and the results indicated that the presence of 35% TFE did indeed induce a more ordered conformation in the central linker, with order parameters for Asp78-Glu80 of 0.29, 0.17, and 0.27 in H(2)O and 0.82, 0.66, and 0.64 in 35% TFE. However, (15)N-[(1)H] NOE values showed that these residues were still slightly more flexible than the rest of the molecule in 35% TFE (Asp78-Glu80 (15)N-[(1)H] NOE=0.46, 0.46, and 0.51). Furthermore, there is still independent motion of the two lobes of Ca(2+)-CaM in 35% TFE, with motional correlation times of approximately 10 and approximately 9 ns for the N- and C-lobes, respectively, indicating that 35% TFE was not sufficient to force Ca(2+)-CaM into a rigid dumbbell-shaped molecule as seen in the crystal structure. Additional factors that could further stabilize the structure of CaM in the crystal include pH, temperature, and crystal packing.
Collapse
Affiliation(s)
- Richard D Brokx
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W., Calgary, Alta., Canada T2N 1N4
| | | | | | | |
Collapse
|
49
|
Yamniuk AP, Vogel HJ. Calmodulin's flexibility allows for promiscuity in its interactions with target proteins and peptides. Mol Biotechnol 2004; 27:33-57. [PMID: 15122046 DOI: 10.1385/mb:27:1:33] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The small bilobal calcium regulatory protein calmodulin (CaM) activates numerous target enzymes in response to transient changes in intracellular calcium concentrations. Binding of calcium to the two helix-loop-helix calcium-binding motifs in each of the globular domains induces conformational changes that expose a methionine-rich hydrophobic patch on the surface of each domain of the protein, which it uses to bind to peptide sequences in its target enzymes. Although these CaM-binding domains typically have little sequence identity, the positions of several bulky hydrophobic residues are often conserved, allowing for classification of CaM-binding domains into recognition motifs, such as the 1-14 and 1-10 motifs. For calcium-independent binding of CaM, a third motif known as the IQ motif is also common. Many CaM-peptide complexes have globular conformations, where CaM's central linker connecting the two domains unwinds, allowing the protein to wrap around a single predominantly alpha-helical target peptide sequence. However, novel structures have recently been reported where the conformation of CaM is highly dissimilar to these globular complexes, in some instances with less than a full compliment of bound calcium ions, as well as novel stoichiometries. Furthermore, many divergent CaM isoforms from yeast and plant species have been discovered with unique calcium-binding and enzymatic activation characteristics compared to the single CaM isoform found in mammals.
Collapse
Affiliation(s)
- Aaron P Yamniuk
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada
| | | |
Collapse
|
50
|
Hobson KF, Housley NA, Pedigo S. Ligand-linked stability of mutants of the C-domain of calmodulin. Biophys Chem 2004; 114:43-52. [PMID: 15792860 DOI: 10.1016/j.bpc.2004.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2004] [Revised: 11/05/2004] [Accepted: 11/05/2004] [Indexed: 10/26/2022]
Abstract
There is a necessary energetic linkage between ligand binding and stability in biological molecules. The critical glutamate in Site 4 was mutated to create two mutants of the C-domain of calmodulin yielding E140D and E140Q. These proteins were stably folded in the absence of calcium, but had dramatically impaired binding of calcium. We determined the stability of the mutant proteins in the absence and presence of calcium using urea-induced unfolding monitored by circular dichroism (CD) spectroscopy. These calcium-dependent unfolding curves were fit to models that allowed for linkage of stability to binding of a single calcium ion to the native and unfolded states. Simultaneous analysis of the unfolding profiles for each mutant yielded estimates for calcium-binding constants that were consistent with results from direct titrations monitored by fluorescence. Binding to the unfolded state was not an important energetic contributor to the ligand-linked stability of these mutants.
Collapse
Affiliation(s)
- Kenosha F Hobson
- University of Mississippi, Dept. of Chemistry and Biochemistry, University, MS 38677, USA
| | | | | |
Collapse
|