1
|
Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes. Methods Mol Biol 2021. [PMID: 32856257 DOI: 10.1007/978-1-0716-0928-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.
Collapse
|
2
|
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: 1.3] [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
|
3
|
Cotranslocational processing of the protein substrate calmodulin by an AAA+ unfoldase occurs via unfolding and refolding intermediates. Proc Natl Acad Sci U S A 2018; 115:E4786-E4795. [PMID: 29735657 DOI: 10.1073/pnas.1721811115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein remodeling by AAA+ enzymes is central for maintaining proteostasis in a living cell. However, a detailed structural description of how this is accomplished at the level of the substrate molecules that are acted upon is lacking. Here, we combine chemical cross-linking and methyl transverse relaxation-optimized NMR spectroscopy to study, at atomic resolution, the stepwise unfolding and subsequent refolding of the two-domain substrate calmodulin by the VAT AAA+ unfoldase from Thermoplasma acidophilum By engineering intermolecular disulphide bridges between the substrate and VAT we trap the substrate at different stages of translocation, allowing structural studies throughout the translocation process. Our results show that VAT initiates substrate translocation by pulling on intrinsically unstructured N or C termini of substrate molecules without showing specificity for a particular amino acid sequence. Although the B1 domain of protein G is shown to unfold cooperatively, translocation of calmodulin leads to the formation of intermediates, and these differ on an individual domain level in a manner that depends on whether pulling is from the N or C terminus. The approach presented generates an atomic resolution picture of substrate unfolding and subsequent refolding by unfoldases that can be quite different from results obtained via in vitro denaturation experiments.
Collapse
|
4
|
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: 3.4] [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
|
5
|
The Ca(2+) influence on calmodulin unfolding pathway: a steered molecular dynamics simulation study. PLoS One 2012; 7:e49013. [PMID: 23145050 PMCID: PMC3492193 DOI: 10.1371/journal.pone.0049013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/08/2012] [Indexed: 11/19/2022] Open
Abstract
The force-induced unfolding of calmodulin (CaM) was investigated at atomistic details with steered molecular dynamics. The two isolated CaM domains as well as the full-length CaM were simulated in N-C-terminal pulling scheme, and the isolated N-lobe of CaM was studied specially in two other pulling schemes to test the effect of pulling direction and compare with relevant experiments. Both Ca2+-loaded CaM and Ca2+-free CaM were considered in order to define the Ca2+ influence to the CaM unfolding. The results reveal that the Ca2+ significantly affects the stability and unfolding behaviors of both the isolated CaM domains and the full-length CaM. In Ca2+-loaded CaM, N-terminal domain unfolds in priori to the C-terminal domain. But in Ca2+-free CaM, the unfolding order changes, and C-terminal domain unfolds first. The force-extension curves of CaM unfolding indicate that the major unfolding barrier comes from conquering the interaction of two EF-hand motifs in both N- and C- terminal domains. Our results provide the atomistic-level insights in the force-induced CaM unfolding and explain the observation in recent AFM experiments.
Collapse
|
6
|
Gibrat G, Assairi L, Craescu CT, Hui Bon Hoa G, Loew D, Lombard B, Blouquit L, Bellissent-Funel MC. Use of SANS and biophysical techniques to reveal subtle conformational differences between native apo-calmodulin and its unfolded states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1097-106. [PMID: 22709575 DOI: 10.1016/j.bbapap.2012.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 05/24/2012] [Accepted: 06/01/2012] [Indexed: 11/16/2022]
Abstract
Apo-calmodulin, a small, mainly α, soluble protein is a calcium-dependent protein activator. It is made of two N- and C-terminal domains having a sequence homology of 70%, an identical folding but different stabilities, and is thus an interesting system for unfolding studies. The use of small angle neutron scattering (SANS) and other biophysical techniques has permitted to reveal conformational difference between native and thermal denatured states of apo-calmodulin. The results show that secondary and tertiary structures of apo-calmodulin evolve in a synchronous way, indicating the absence in the unfolding pathway of molten-globule state sufficiently stable to affect transition curves. From SANS experiments, at 85 °C, apo-calmodulin adopts a polymer chain conformation with some residual local structures. After cooling down, apo-calmodulin recovers a compact state, with a secondary structure close to the native one but with a higher radius of gyration and a different tyrosine environment. In fact on a timescale of few minutes, heat denaturation of apo-calmodulin is partially reversible, but on a time scale of hours (for SANS experiments), the long exposure to heat may lead to a non-reversibility due to some chemical perturbation of the protein. In fact, from Mass Spectrometry measurements, we got evidence of dehydration and deamidation of heated apo-calmodulin.
Collapse
|
7
|
Kleinjung J, Scott WRP, Allison JR, van Gunsteren WF, Fraternali F. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations. J Chem Theory Comput 2012. [PMID: 23180979 PMCID: PMC3503459 DOI: 10.1021/ct200390j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Implicit solvation is a mean force approach to model
solvent forces
acting on a solute molecule. It is frequently used in molecular simulations
to reduce the computational cost of solvent treatment. In the first
instance, the free energy of solvation and the associated solvent–solute
forces can be approximated by a function of the solvent-accessible
surface area (SASA) of the solute and differentiated by an atom–specific
solvation parameter σiSASA. A procedure
for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation
forces is proposed. Using the results of Molecular Dynamics simulations
of 188 topologically diverse protein structures in water and in implicit
solvent, values for the σiSASA parameters
for atom types i of the standard amino acids in the
GROMOS force field have been determined. A simplified representation
based on groups of atom types σgSASA was
obtained via partitioning of the atom–type
σiSASA distributions by dynamic programming.
Three groups of atom types with well separated parameter ranges were
obtained, and their performance in implicit versus explicit simulations
was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces.
Collapse
Affiliation(s)
- Jens Kleinjung
- Division of Mathematical Biology, MRC National Institute for Medical Research , The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | | | | | | | | |
Collapse
|
8
|
Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Methods Mol Biol 2012; 819:375-92. [PMID: 22183548 DOI: 10.1007/978-1-61779-465-0_23] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The effects of solvation on molecular recognition are investigated from different perspectives, ranging from methods to analyse explicit solvent dynamical behaviour at the protein surface to methods for the implicit treatment of solvent effects associated with the conformational behaviour of biomolecules. The here presented implicit solvation method is based on an analytical approximation of the Solvent Accessible Surface Area (SASA) of solute molecules, which is computationally efficient and easy to parametrise. The parametrised SASA solvation method is discussed in the light of protein design and ligand binding studies. The POPS program for the SASA computation on single molecules and complex interfaces is described in detail. Explicit solvent behaviour is described here in the form of solvent density maps at the protein surface. We highlight the usefulness of that approach in defining the organisation of specific water molecules at functional sites and in determining hydrophobicity scores for the identification of potential interaction patches.
Collapse
|
9
|
The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLoS Comput Biol 2011; 7:e1002114. [PMID: 21829336 PMCID: PMC3145654 DOI: 10.1371/journal.pcbi.1002114] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/23/2011] [Indexed: 11/20/2022] Open
Abstract
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.
Collapse
|
10
|
Biophysical study of thermal denaturation of apo-calmodulin: dynamics of native and unfolded states. Biophys J 2008; 95:5247-56. [PMID: 18223007 DOI: 10.1529/biophysj.107.120147] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apo-calmodulin, a small, mainly alpha, soluble protein is a calcium-dependent protein activator. This article presents a study of internal dynamics of native and thermal unfolded apo-calmodulin, using quasi-elastic neutron scattering. This technique can probe protein internal dynamics in the picosecond timescale and in the nanometer length-scale. It appears that a dynamical transition is associated with thermal denaturation of apo-calmodulin. This dynamical transition goes together with a decrease of the confinement of hydrogen atoms, a decrease of immobile protons proportion and an increase of dynamical heterogeneity. The comparison of native and unfolded states dynamics suggests that the dynamics of protein atoms is more influenced by their distance to the backbone than by their solvent exposure.
Collapse
|
11
|
Christen M, van Gunsteren WF. On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. J Comput Chem 2007; 29:157-66. [PMID: 17570138 DOI: 10.1002/jcc.20725] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Methods to search for low-energy conformations, to generate a Boltzmann-weighted ensemble of configurations, or to generate classical-dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest.
Collapse
Affiliation(s)
- Markus Christen
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, CH-8093 Zürich, Switzerland
| | | |
Collapse
|
12
|
Lei H, Duan Y. The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J Chem Phys 2006; 121:12104-11. [PMID: 15634176 DOI: 10.1063/1.1822916] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.
Collapse
Affiliation(s)
- Hongxing Lei
- Bioinformatics Program and Department of Applied Science, University of California, Davis, California 95616, USA
| | | |
Collapse
|
13
|
Vaccaro L, Cross KJ, Kleinjung J, Straus SK, Thomas DJ, Wharton SA, Skehel JJ, Fraternali F. Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers. Biophys J 2004; 88:25-36. [PMID: 15475582 PMCID: PMC1305003 DOI: 10.1529/biophysj.104.044537] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A detailed molecular dynamics study of the haemagglutinin fusion peptide (N-terminal 20 residues of the HA2 subunits) in a model bilayer has yielded useful information about the molecular interactions leading to insertion into the lipids. Simulations were performed on the native sequence, as well as a number of mutant sequences, which are either fusogenic or nonfusogenic. For the native sequence and fusogenic mutants, the N-terminal 11 residues of the fusion peptides are helical and insert with a tilt angle of approximately 30 degrees with respect to the membrane normal, in very good agreement with experimental data. The tilted insertion of the native sequence peptide leads to membrane bilayer thinning and the calculated order parameters show larger disorder of the alkyl chains. These results indicate that the lipid packing is perturbed by the fusion peptide and could be used to explain membrane fusion. For the nonfusogenic sequences investigated, it was found that most of them equilibrate parallel to the interface plane and do not adopt a tilted conformation. The presence of a charged residue at the beginning of the sequence (G1E mutant) resulted in a more difficult case, and the outcomes do not fall straightforwardly into the general picture. Sequence searches have revealed similarities of the fusion peptide of influenza haemagglutinin with peptide sequences such as segments of porin, amyloid alpha eta peptide, and a peptide from the prion sequence. These results confirm that the sequence can adopt different folds in different environments. The plasticity and the conformational dependence on the local environment could be used to better understand the function of fusion peptides.
Collapse
Affiliation(s)
- Loredana Vaccaro
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Karen J. Cross
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Jens Kleinjung
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Suzana K. Straus
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - David J. Thomas
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Stephen A. Wharton
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - John J. Skehel
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| | - Franca Fraternali
- National Institute for Medical Research, London, United Kingdom; Bioinformatics Unit, Faculty of Sciences, Free University of Amsterdam, Amsterdam, The Netherlands; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; and Biological Nuclear Magnetic Resonance Unit, Institute for Clinical Research, Medical School, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
14
|
Schumacher MA, Crum M, Miller MC. Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex. Structure 2004; 12:849-60. [PMID: 15130477 DOI: 10.1016/j.str.2004.03.017] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Revised: 02/19/2004] [Accepted: 03/02/2004] [Indexed: 11/24/2022]
Abstract
Small conductance Ca2+-activated K+ channels (SK channels) are composed of the pore-forming alpha subunit and calmodulin (CaM). CaM binds to a region of the alpha subunit called the CaM binding domain (CaMBD), located intracellular and immediately C-terminal to the inner helix gate, in either the presence or absence of Ca2+. SK gating occurs when Ca2+ binds the N lobe of CaM thereby transmitting the signal to the attached inner helix gate to open. Here we present crystal structures of apoCaM and apoCaM/SK2 CaMBD complex. Several apoCaM crystal forms with multiple (12) packing environments reveal the same EF hand domain-swapped dimer providing potentially new insight into CaM regulation. The apoCaM/SK2 CaMBD structure, combined with our Ca2+/CaM/CaMBD structure suggests that Ca2+ binding induces folding and dimerization of the CaMBD, which causes large CaMBD-CaM C lobe conformational changes, including a >90 degrees rotation of the region of the CaMBD directly connected to the gate.
Collapse
Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239 USA.
| | | | | |
Collapse
|
15
|
Zuckerman DM. Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin. J Phys Chem B 2004. [DOI: 10.1021/jp0370730] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel M. Zuckerman
- Center for Computational Biology & Bioinformatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, and Department of Environmental & Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| |
Collapse
|