1
|
Cukier RI. Simulations of Potentials of Mean Force for Separating a Leucine Zipper Dimer and the Basic Region of a Basic Region Leucine Zipper Dimer. J Phys Chem B 2014; 118:10341-54. [DOI: 10.1021/jp504723m] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Robert I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| |
Collapse
|
2
|
Molecular Modeling of PEGylated Peptides, Dendrimers, and Single-Walled Carbon Nanotubes for Biomedical Applications. Polymers (Basel) 2014. [DOI: 10.3390/polym6030776] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
|
3
|
Oshaben KM, Salari R, McCaslin DR, Chong LT, Horne WS. The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state. Biochemistry 2012; 51:9581-91. [PMID: 23116373 DOI: 10.1021/bi301132k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The dimerization domain of the yeast transcription factor GCN4, one of the first coiled-coil proteins to be structurally characterized at high resolution, has served as the basis for numerous fundamental studies on α-helical folding. Mutations in the GCN4 leucine zipper are known to change its preferred oligomerization state from dimeric to trimeric or tetrameric; however, the wild-type sequence has been assumed to encode a two-chain assembly exclusively. Here we demonstrate that the GCN4 coiled-coil domain can populate either a dimer or trimer fold, depending on environment. We report high-resolution crystal structures of the wild-type sequence in dimeric and trimeric assemblies. Biophysical measurements suggest populations of both oligomerization states under certain experimental conditions in solution. We use parallel tempering molecular dynamics simulations on the microsecond time scale to compare the stability of the dimer and trimer folded states in isolation. In total, our results suggest that the folding behavior of the well-studied GCN4 leucine-zipper domain is more complex than was previously appreciated. Our results have implications in ongoing efforts to establish predictive algorithms for coiled-coil folds and the selection of coiled-coil model systems for design and mutational studies where oligomerization state specificity is an important consideration.
Collapse
Affiliation(s)
- Kaylyn M Oshaben
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | | | | | | |
Collapse
|
4
|
Cukier RI. Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper. J Phys Chem B 2012; 116:6071-86. [PMID: 22559083 DOI: 10.1021/jp300836t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Basic region leucine zipper (bZIP) transcription factors are dimeric proteins that recognize DNA. The monomers consist of a leucine zipper subdomain responsible for dimerization and a highly basic DNA recognition subdomain. Twelve explicit solvent molecular dynamics (MD) trajectories were run on the GCN4 bZIP transcriptional factor in the absence of DNA at three temperatures and two ion concentrations (0 mM with Cl(-) ions to neutralize the bZIP and 200 mM with additional Na(+) and Cl(-) ions) to probe the conformational ensemble that the basic region samples. In most trajectories, the basic region exhibits an alligator-jaw-like opening and closing (only one monomer moves), versus scissor-like motion, by a mainly rigid body, hinge motion centered on three "fork" residues that span the basic region to the coiled coil. In this motion, the α-helical character of the basic region monomers is mostly maintained. A broad range of distances is accessed, consistent with the absence of particular interactions for the basic region monomers. In two of the trajectories, the basic region monomers "collapse" to form a stable state. The coiled coil, leucine zipper subdomain is very stable for all of the trajectories. Ion solvation of the charged residue side chains is transient, on the scale of a few picoseconds. There is no evidence for persistent specific ion salt bridges to charged residues. For 0 mM, only certain basic region positively charged residues are substantially Cl(-) ion salt bridged. For 200 mM, in addition, some basic region negatively (positively) charged residues are salt bridged to Na(+) (Cl(-)) ions. The different ion solvation patterns at the two ion concentrations are not greatly temperature sensitive, and the conformational sampling found in the MD is remarkably unperturbed by ion concentration and/or temperature.
Collapse
Affiliation(s)
- Robert I Cukier
- Department of Chemistry Michigan State University, East Lansing, 48824-1322, United States.
| |
Collapse
|
5
|
Dolenc J, Missimer JH, Steinmetz MO, van Gunsteren WF. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1. JOURNAL OF BIOMOLECULAR NMR 2010; 47:221-235. [PMID: 20524044 DOI: 10.1007/s10858-010-9425-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 04/21/2010] [Indexed: 05/29/2023]
Abstract
The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 phi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and (3)J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and (3)J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.
Collapse
Affiliation(s)
- Jozica Dolenc
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093, Zürich, Switzerland
| | | | | | | |
Collapse
|
6
|
Liu Y, Chapagain PP, Gerstman BS. Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine Dimer. J Phys Chem B 2009; 114:796-803. [DOI: 10.1021/jp909872a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yanxin Liu
- Department of Physics, Florida International University, University Park, Miami, Florida 33199
| | - Prem P. Chapagain
- Department of Physics, Florida International University, University Park, Miami, Florida 33199
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, University Park, Miami, Florida 33199
| |
Collapse
|
7
|
Su L, Cukier RI. Hamiltonian Replica Exchange Method Studies of a Leucine Zipper Dimer. J Phys Chem B 2009; 113:9595-605. [DOI: 10.1021/jp900309q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li Su
- Department of Chemistry and the Quantitative Biology Modeling Initiative Michigan State University, East Lansing, Michigan 48824
| | - Robert I. Cukier
- Department of Chemistry and the Quantitative Biology Modeling Initiative Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
8
|
Sharma G, Mavroidis C, Rege K, Yarmush ML, Budil D. Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications. Int J Rob Res 2009. [DOI: 10.1177/0278364908100278] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The design hypothesis, architectures, and computational modeling of a novel peptide-based nanoactuator are presented in this paper. We engineered the α-helical coiled-coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally responsive nanoactuator. The dimeric coiled-coil peptide consists of two identical approximately 4.5 nm long and approximately 3 nm wide polypeptide chains. The actuation mechanism depends on the modification of electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and, therefore, creating the motion of an actuator. Using molecular dynamics simulations we showed that pH changes led to a reversible opening of up to 1.5 nm which is approximately 150% of the initial separation of the nanoactuator. We also investigated the forces generated by the nanoactuator upon pH actuation, using a new method based on a modified steered molecular dynamics technique. Owing to its open and close motion resembling that of tweezers, the new nanoactuator can potentially be used as a nanogripper in various nanomanipulation tasks such as detection and removal of heavy metal ions during nanofabrication processes or as a molecular switch.
Collapse
Affiliation(s)
- Gaurav Sharma
- Department of Mechanical and Industrial Engineering, 360 Huntington Avenue, Northeastern University, Boston, MA 02115, USA
| | - Constantinos Mavroidis
- Department of Mechanical and Industrial Engineering, 360 Huntington Avenue, Northeastern University, Boston, MA 02115, USA,
| | - Kaushal Rege
- The Center for Engineering in Medicine (CEM), Massachusetts General Hospital and Harvard Medical School, 51 Blossom Street, Boston, MA 02114, USA, Department of Chemical Engineering, Arizona State University, Tempe, AZ, USA
| | - Martin L. Yarmush
- The Center for Engineering in Medicine (CEM), Massachusetts General Hospital and Harvard Medical School, 51 Blossom Street, Boston, MA 02114, USA
| | - David Budil
- Department of Chemistry and Chemical Biology, 60 Huntington Avenue, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
9
|
Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins 2009; 74:612-29. [PMID: 18704948 PMCID: PMC2692595 DOI: 10.1002/prot.22177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. To better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. We also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein structure. Molecular dynamics (MD) and free energy simulations with AMBER used a particle mesh Ewald treatment of the electrostatics in explicit TIP3P solvent with balanced force field treatments. Preliminary studies with legacy force fields (ff94, ff96, and ff99) show a profound instability of the coiled-coil structures in short MD simulation. Significantly, better behavior is evident with the more balanced ff99SB and ff03 protein force fields. Overall, the results suggest that the coiled-coil structures can readily accommodate the larger acidic arginine or S-2,7-diaminoheptanedoic acid mutants in the salt bridge, whereas substitution of the smaller L-ornithine residue leads to rapid disruption of the coiled-coil structure on the MD simulation time scale. This structural distortion of the secondary structure allows both the formation of large hydration pockets proximal to the charged groups and within the hydrophobic core. Moreover, the increased structural fluctuations and movement lead to a decrease in the water occupancy lifetimes in the hydration pockets. In contrast, analysis of the hydration in the stable dimeric coiled-coils shows high occupancy water sites along the backbone residues with no water occupancy in the hydrophobic core, although transitory water interactions with the salt bridge residues are evident. The simulations of the fluorinated coiled-coils suggest that in some cases fluorination electrostatically stabilizes the intermolecular coiled-coil salt bridges. Structural analyses also reveal different side chain rotamer preferences for leucine when compared with 5,5,5,5',5',5'-hexafluoroleucine mutants. These observed differences in the side chain rotamer populations suggest differential changes in the side chain conformational entropy upon coiled-coil formation when the protein is fluorinated. The free energy of hydration of the isolated 5,5,5,5',5',5'-hexafluoroleucine amino acid is calculated to be 1.1 kcal/mol less stable than leucine; this hydrophobic penalty in the monomer may provide a driving force for coiled-coil dimer formation. Estimation of the ellipticity at 222 nm from a series of snapshots from the MD simulations with DicroCalc shows distinct increases in the ellipticity when the coiled-coil is fluorinated, which suggests that the helicity in the folded coiled-coils is greater when fluorinated.
Collapse
Affiliation(s)
- Scott S. Pendley
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| | - Yihua B. Yu
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Departments of Pharmaceutical Sciences and Bioengineering, University of Maryland, University of Maryland, 20 Penn Street, Rm. 635, Baltimore, MD 21201
| | - Thomas E. Cheatham
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Medicinal Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Bioengineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| |
Collapse
|
10
|
Chapagain PP, Liu Y, Gerstman BS. The trigger sequence in the GCN4 leucine zipper: α-helical propensity and multistate dynamics of folding and dimerization. J Chem Phys 2008; 129:175103. [DOI: 10.1063/1.3006421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
11
|
Sharma G, Rege K, Budil DE, Yarmush ML, Mavroidis C. Reversible pH-controlled DNA-binding peptide nanotweezers: an in-silico study. Int J Nanomedicine 2008; 3:505-21. [PMID: 19337419 PMCID: PMC2636583 DOI: 10.2147/ijn.s4046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We describe the molecular dynamics (MD)-aided engineering design of mutant
peptides based on the α-helical coiled-coil GCN4 leucine zipper
peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers.
The actuation mechanism of the nanotweezers depends on the modification of
electrostatic charges on the residues along the length of the coiled coil.
Modulating the solution pH between neutral and acidic values results in the
reversible movement of helices toward and away from each other and creates a
complete closed-open-closed transition cycle between the helices. Our results
indicate that the mutants show a reversible opening of up to 15 Å
(1.5 nm; approximately 150% of the initial separation) upon pH
actuation. Investigation on the physicochemical phenomena that influence
conformational properties, structural stability, and reversibility of the
coiled-coil peptide-based nanotweezers revealed that a rationale- and
design-based approach is needed to engineer stable peptide or macromolecules
into stimuli-responsive devices. The efficacy of the mutant that demonstrated
the most significant reversible actuation for environmentally responsive
modulation of DNA-binding activity was also demonstrated. Our results have
significant implications in bioseparations and in the engineering of novel
transcription factors.
Collapse
Affiliation(s)
- Gaurav Sharma
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | | | | | | | | |
Collapse
|
12
|
Missimer JH, Steinmetz MO, Baron R, Winkler FK, Kammerer RA, Daura X, van Gunsteren WF. Configurational entropy elucidates the role of salt-bridge networks in protein thermostability. Protein Sci 2007; 16:1349-59. [PMID: 17586770 PMCID: PMC2206687 DOI: 10.1110/ps.062542907] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Detailed knowledge of how networks of surface salt bridges contribute to protein thermal stability is essential not only to understand protein structure and function but also to design thermostable proteins for industrial applications. Experimental studies investigating thermodynamic stability through measurements of free energy associated with mutational alterations in proteins provide only macroscopic evidence regarding the structure of salt-bridge networks and assessment of their contribution to protein stability. Using explicit-solvent molecular dynamics simulations to provide insight on the atomic scale, we investigate here the structural stability, defined in terms of root-mean-square fluctuations, of a short polypeptide designed to fold into a stable trimeric coiled coil with a well-packed hydrophobic core and an optimal number of intra- and interhelical surface salt bridges. We find that the increase of configurational entropy of the backbone and side-chain atoms and decreased pair correlations of these with increased temperature are consistent with nearly constant atom-positional root-mean-square fluctuations, increased salt-bridge occupancies, and stronger electrostatic interactions in the coiled coil. Thus, our study of the coiled coil suggests a mechanism in which well-designed salt-bridge networks could accommodate stochastically the disorder of increased thermal motion to produce thermostability.
Collapse
Affiliation(s)
- John H Missimer
- Biomolecular Research, Structural Biology Paul Scherrer Institut, Villigen, Switzerland.
| | | | | | | | | | | | | |
Collapse
|
13
|
Lee H, Larson RG. Prediction of the stability of coiled coils using molecular dynamics simulations. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020701370612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
14
|
Steinmetz MO, Jelesarov I, Matousek WM, Honnappa S, Jahnke W, Missimer JH, Frank S, Alexandrescu AT, Kammerer RA. Molecular basis of coiled-coil formation. Proc Natl Acad Sci U S A 2007; 104:7062-7. [PMID: 17438295 PMCID: PMC1855353 DOI: 10.1073/pnas.0700321104] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Indexed: 11/18/2022] Open
Abstract
Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed "trigger sequence," that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.
Collapse
Affiliation(s)
- Michel O. Steinmetz
- *Biomolecular Research, Structural Biology, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Ilian Jelesarov
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - William M. Matousek
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125
| | - Srinivas Honnappa
- *Biomolecular Research, Structural Biology, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Wolfgang Jahnke
- Central Technologies, Novartis Pharma AG, CH-4002 Basel, Switzerland
| | - John H. Missimer
- *Biomolecular Research, Structural Biology, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | - Sabine Frank
- F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland; and
| | - Andrei T. Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125
| | - Richard A. Kammerer
- **Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| |
Collapse
|