1
|
Gurusaran M, Zhang J, Zhang K, Shibuya H, Davies OR. MEILB2-BRME1 forms a V-shaped DNA clamp upon BRCA2-binding in meiotic recombination. Nat Commun 2024; 15:6552. [PMID: 39095423 PMCID: PMC11297322 DOI: 10.1038/s41467-024-50920-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
DNA double-strand break repair by homologous recombination has a specialised role in meiosis by generating crossovers that enable the formation of haploid germ cells. This requires meiosis-specific MEILB2-BRME1, which interacts with BRCA2 to facilitate loading of recombinases onto resected DNA ends. Here, we report the crystal structure of the MEILB2-BRME1 2:2 core complex, revealing a parallel four-helical assembly that recruits BRME1 to meiotic double-strand breaks in vivo. It forms an N-terminal β-cap that binds to DNA, and a MEILB2 coiled-coil that bridges to C-terminal ARM domains. Upon BRCA2-binding, MEILB2-BRME1 2:2 complexes dimerize into a V-shaped 2:4:4 complex, with rod-like MEILB2-BRME1 components arranged at right-angles. The β-caps located at the tips of the MEILB2-BRME1 limbs are separated by 25 nm, allowing them to bridge between DNA molecules. Thus, we propose that BRCA2 induces MEILB2-BRME1 to function as a DNA clamp, connecting resected DNA ends or homologous chromosomes to facilitate meiotic recombination.
Collapse
Affiliation(s)
- Manickam Gurusaran
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Jingjing Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kexin Zhang
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Laboratory for Gametogenesis, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan
| | - Owen R Davies
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
2
|
Carder J, Barile B, Shisler KA, Pisani F, Frigeri A, Hipps KW, Nicchia GP, Brozik JA. Thermodynamics and S-Palmitoylation Dependence of Interactions between Human Aquaporin-4 M1 Tetramers in Model Membranes. J Phys Chem B 2024; 128:603-621. [PMID: 38212942 PMCID: PMC10824246 DOI: 10.1021/acs.jpcb.3c04529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/09/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
Aquaporin-4 (AQP4) is a water channel protein found primarily in the central nervous system (CNS) that helps to regulate water-ion homeostasis. AQP4 exists in two major isoforms: M1 and M23. While both isoforms have a homotetrameric quaternary structure and are functionally identical when transporting water, the M23 isoform forms large protein aggregates known as orthogonal arrays of particles (OAPs). In contrast, the M1 isoform creates a peripheral layer around the outside of these OAPs, suggesting a thermodynamically stable interaction between the two. Structurally, the M1 isoform has an N-terminal tail that is 22 amino acids longer than the M23 isoform and contains two solvent-accessible cysteines available for S-palmitoylation at cysteine-13 (Cys-13) and cysteine-17 (Cys-17) in the amino acid sequence. Earlier work suggests that the palmitoylation of these cysteines might aid in regulating AQP4 assemblies. This work discusses the thermodynamic driving forces for M1 protein-protein interactions and how the palmitoylation state of M1 affects them. Using temperature-dependent single-particle tracking, the standard state free energies, enthalpies, and entropies were measured for these interactions. Furthermore, we present a binding model based on measured thermodynamics and a structural modeling study. The results of this study demonstrate that the M1 isoform will associate with itself according to the following expressions: 2[AQP4-M1]4 ↔ [[AQP4-M1]4]2 when palmitoylated and 3[AQP4-M1]4 ↔ [AQP4-M1]4 + [[AQP4-M1]4]2 ↔ [[AQP4-M1]4]3 when depalmitoylated. This is primarily due to a conformational change induced by adding the palmitic acid groups at Cys-13 and Cys-17 in the N-terminal tails of the homotetramers. In addition, a statistical mechanical model was developed to estimate the Gibbs free energy, enthalpy, and entropy for forming dimers and trimers. These results were in good agreement with experimental values.
Collapse
Affiliation(s)
- Jessica
D. Carder
- Department
of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164-4630, United States
| | - Barbara Barile
- Department
of Bioscience, Biotechnologies and Environment, University of Bari Aldo Moro, Bari 70124, Italy
| | - Krista A. Shisler
- Department
of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164-4630, United States
| | - Francesco Pisani
- Department
of Bioscience, Biotechnologies and Environment, University of Bari Aldo Moro, Bari 70124, Italy
| | - Antonio Frigeri
- Department
of Translational Medicine and Neuroscience, University of Bari Aldo Moro, Bari 70124, Italy
- Dominick
P. Purpura Department of Neuroscience, Albert
Einstein College of Medicine, 840 Kennedy Center, Bronx, New York 10461, United States
| | - K. W. Hipps
- Department
of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164-4630, United States
- Materials
Science & Engineering Program, Washington
State University, Pullman, Washington 99163-2711, United States
| | - Grazia Paola Nicchia
- Department
of Bioscience, Biotechnologies and Environment, University of Bari Aldo Moro, Bari 70124, Italy
- Dominick
P. Purpura Department of Neuroscience, Albert
Einstein College of Medicine, 840 Kennedy Center, Bronx, New York 10461, United States
| | - James A. Brozik
- Department
of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164-4630, United States
- Materials
Science & Engineering Program, Washington
State University, Pullman, Washington 99163-2711, United States
| |
Collapse
|
3
|
Xia H, Xu H, Wang J, Wang C, Chen R, Tao T, Xu S, Zhang J, Ma K, Wang J. Heat sensitive E-helix cut ferritin nanocages for facile and high-efficiency loading of doxorubicin. Int J Biol Macromol 2023; 253:126973. [PMID: 37729988 DOI: 10.1016/j.ijbiomac.2023.126973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023]
Abstract
Ferritin possesses a stable and uniform cage structure, along with tumor-targeting properties and excellent biocompatibility, making it a promising drug delivery vehicle. However, the current ferritin drug loading strategy involves complex steps and harsh reaction conditions, resulting in low yield and recovery of drug loading, which limits the clinical application prospects of ferritin nanomedicine. In this study, we utilized the high-efficiency heat-sensitivity of the multiple channel switch structures of the E-helix-cut ferritin mutant (Ecut-HFn) and Cu2+ assistance to achieve high-efficiency loading of chemotherapeutic drugs in a one-step process at low temperatures. This method features mild reaction conditions (45 °C), high loading efficiency (about 110 doxorubicin (Dox) per Ecut-HFn), and improved protein and Dox recovery rates (with protein recovery rate around 94 % and Dox recovery rate reaching up to 45 %). The prepared ferritin-Dox particles (Ecut-HFn-Cu-Dox) exhibit a uniform size distribution, good stability, and retain the natural tumor targeting ability of ferritin. Overall, this temperature-controlled drug loading strategy utilizing heat-sensitivity ferritin mutants is energy-saving, environmentally friendly, efficient, and easy to operate, offering a new perspective for scaling up the industrial production of ferritin drug carriers.
Collapse
Affiliation(s)
- Haining Xia
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Huangtao Xu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Jiarong Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Changhao Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Ruiguo Chen
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Tongxiang Tao
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Shuai Xu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China
| | - Jing Zhang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China
| | - Kun Ma
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China.
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, PR China; University of Science and Technology of China, Hefei 230026, PR China; Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, PR China.
| |
Collapse
|
4
|
Behbahanipour M, García-Pardo J, Ventura S. Decoding the role of coiled-coil motifs in human prion-like proteins. Prion 2021; 15:143-154. [PMID: 34428113 PMCID: PMC8386614 DOI: 10.1080/19336896.2021.1961569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/28/2022] Open
Abstract
Prions are self-propagating proteins that cause fatal neurodegenerative diseases in humans. However, increasing evidence suggests that eukaryotic cells exploit prion conformational conversion for functional purposes. A recent study delineated a group of twenty prion-like proteins in humans, characterized by the presence of low-complexity glutamine-rich sequences with overlapping coiled-coil (CCs) motifs. This is the case of Mediator complex subunit 15 (MED15), which is overexpressed in a wide range of human cancers. Biophysical studies demonstrated that the prion-like domain (PrLD) of MED15 forms homodimers in solution, sustained by CCs interactions. Furthermore, the same coiled-coil (CC) region plays a crucial role in the PrLD structural transition to a transmissible β-sheet amyloid state. In this review, we discuss the role of CCs motifs and their contribution to amyloid transitions in human prion-like domains (PrLDs), while providing a comprehensive overview of six predicted human prion-like proteins involved in transcription, gene expression, or DNA damage response and associated with human disease, whose PrLDs contain or overlap with CCs sequences. Finally, we try to rationalize how these molecular signatures might relate to both their function and involvement in disease.
Collapse
Affiliation(s)
- Molood Behbahanipour
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Javier García-Pardo
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| |
Collapse
|
5
|
Biok NA, Passow AD, Wang C, Bingman CA, Abbott NL, Gellman SH. Retention of Coiled-Coil Dimer Formation in the Absence of Ion Pairing at Positions Flanking the Hydrophobic Core. Biochemistry 2019; 58:4821-4826. [DOI: 10.1021/acs.biochem.9b00668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Naomi A. Biok
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Alexander D. Passow
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chenxuan Wang
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca, New York 14853, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
6
|
Lathbridge A, Mason JM. Combining Constrained Heptapeptide Cassettes with Computational Design To Create Coiled-Coil Targeting Helical Peptides. ACS Chem Biol 2019; 14:1293-1304. [PMID: 31117396 DOI: 10.1021/acschembio.9b00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A total of 32 heptapeptides have been synthesized and characterized to establish the effect of K → D (i → i + 4) lactamization upon their ability to adopt a helical conformation. Because most parallel and dimeric coiled-coil sequences can be deconvoluted into gabcdef repeats, we have introduced fixed solvent exposed b → f (K → D) constraints into this design scaffold. Interfacial " a" hydrophobic (L/I/V/N) and " e/g" electrostatic (E/K) options (4 × 2 × 2 = 16 cassettes) were introduced as core drivers of coiled-coil stability and specificity. All present as random coils when linear but adopt a helical conformation upon lactamization. Helicity varied in magnitude from 34 to 68%, indicating different levels of constraint tolerance within the context of a sequence required to be helical for function. Using the oncogenic transcription factor cJun as an exemplar, we next utilized our bCIPA coiled-coil screening engine to select four cassettes of highest predicted affinity when paired with four gabcdef cassettes within the full-length cJun target counterpart (164 = 65 536 combinations). This information was coupled with observed helicity for each constrained cassette to select for the best balance of predicted affinity when linear and experimentally validated helicity when constrained. As a control, the same approach was taken using cassettes of high predicted target affinity but with lower experimentally validated helicity. The approach provides a novel platform of modular heptapeptide cassettes experimentally validated and separated by helical content. Appropriate cassettes can be selected and conjugated to produce longer peptides, in which constraints impart appropriate helicity such that a wide range of targets can be engaged with high affinity and selectivity.
Collapse
|
7
|
Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation. Biochim Biophys Acta Gen Subj 2018; 1862:2846-2861. [DOI: 10.1016/j.bbagen.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/31/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022]
|
8
|
Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill. Proc Natl Acad Sci U S A 2018; 115:E7905-E7913. [PMID: 30012616 DOI: 10.1073/pnas.1805442115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Influenza hemagglutinin (HA) mediates viral entry into host cells through a large-scale conformational rearrangement at low pH that leads to fusion of the viral and endosomal membranes. Crystallographic and biochemical data suggest that a loop-to-coiled-coil transition of the B-loop region of HA is important for driving this structural rearrangement. However, the microscopic picture for this proposed "spring-loaded" movement is missing. In this study, we focus on understanding the transition of the B loop and perform a set of all-atom molecular dynamics simulations of the full B-loop trimeric structure with the CHARMM36 force field. The free-energy profile constructed from our simulations describes a B loop that stably folds half of the postfusion coiled coil in tens of microseconds, but the full coiled coil is unfavorable. A buried hydrophilic residue, Thr59, is implicated in destabilizing the coiled coil. Interestingly, this conserved threonine is the only residue in the B loop that strictly differentiates between the group 1 and 2 HA molecules. Microsecond-scale constant temperature simulations revealed that kinetic traps in the structural switch of the B loop can be caused by nonnative, intramonomer, or intermonomer β-sheets. The addition of the A helix stabilized the postfusion state of the B loop, but introduced the possibility for further β-sheet structures. Overall, our results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.
Collapse
|
9
|
Baxter D, Perry SR, Hill TA, Kok WM, Zaccai NR, Brady RL, Fairlie DP, Mason JM. Downsizing Proto-oncogene cFos to Short Helix-Constrained Peptides That Bind Jun. ACS Chem Biol 2017. [PMID: 28636317 DOI: 10.1021/acschembio.7b00303] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components. Structural integrity in the presence and absence of Jun was assessed by circular dichroism spectroscopy, while the thermodynamics of binding to cFos was measured by isothermal titration calorimetry. A 25-residue constrained peptide, one-third shorter yet 25% more helical than the structurally characterized 37-residue Fos-derived peptide, retained 80% of the binding free energy as a result of preorganization in a Jun-binding helix conformation, with the entropy gain (TΔS = +3.2 kcal/mol) compensating for the enthalpy loss. Attaching a cell-penetrating peptide (TAT48-57) and a nuclear localization signal (SV40) promoted cell uptake, localization to the nucleus, and inhibition of the proliferation of two breast cancer cell lines.
Collapse
Affiliation(s)
- Daniel Baxter
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Samuel R. Perry
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - W. Mei Kok
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nathan R. Zaccai
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - R. Leo Brady
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Australian Research Council Centre
of Excellence in Advanced Molecular Imaging, Institute for Molecular
Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jody M. Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| |
Collapse
|
10
|
Rabe M, Aisenbrey C, Pluhackova K, de Wert V, Boyle AL, Bruggeman DF, Kirsch SA, Böckmann RA, Kros A, Raap J, Bechinger B. A Coiled-Coil Peptide Shaping Lipid Bilayers upon Fusion. Biophys J 2016; 111:2162-2175. [PMID: 27851940 PMCID: PMC5113151 DOI: 10.1016/j.bpj.2016.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/08/2016] [Accepted: 10/06/2016] [Indexed: 12/19/2022] Open
Abstract
A system based on two designed peptides, namely the cationic peptide K, (KIAALKE)3, and its complementary anionic counterpart called peptide E, (EIAALEK)3, has been used as a minimal model for membrane fusion, inspired by SNARE proteins. Although the fact that docking of separate vesicle populations via the formation of a dimeric E/K coiled-coil complex can be rationalized, the reasons for the peptides promoting fusion of vesicles cannot be fully explained. Therefore it is of significant interest to determine how the peptides aid in overcoming energetic barriers during lipid rearrangements leading to fusion. In this study, investigations of the peptides' interactions with neutral PC/PE/cholesterol membranes by fluorescence spectroscopy show that tryptophan-labeled K∗ binds to the membrane (KK∗ ∼6.2 103 M-1), whereas E∗ remains fully water-solvated. 15N-NMR spectroscopy, depth-dependent fluorescence quenching, CD-spectroscopy experiments, and MD simulations indicate a helix orientation of K∗ parallel to the membrane surface. Solid-state 31P-NMR of oriented lipid membranes was used to study the impact of peptide incorporation on lipid headgroup alignment. The membrane-immersed K∗ is found to locally alter the bilayer curvature, accompanied by a change of headgroup orientation relative to the membrane normal and of the lipid composition in the vicinity of the bound peptide. The NMR results were supported by molecular dynamics simulations, which showed that K reorganizes the membrane composition in its vicinity, induces positive membrane curvature, and enhances the lipid tail protrusion probability. These effects are known to be fusion relevant. The combined results support the hypothesis for a twofold role of K in the mechanism of membrane fusion: 1) to bring opposing membranes into close proximity via coiled-coil formation and 2) to destabilize both membranes thereby promoting fusion.
Collapse
Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands.
| | | | - Kristyna Pluhackova
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vincent de Wert
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Aimee L Boyle
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Didjay F Bruggeman
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Sonja A Kirsch
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Kros
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Jan Raap
- Leiden Institute of Chemistry - Supramolecular and Biomaterials Chemistry, Leiden University, Leiden, the Netherlands
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS UMR7177, Institut de Chimie, Strasbourg, France.
| |
Collapse
|
11
|
Gáspári Z, Nyitray L. Coiled coils as possible models of protein structure evolution. Biomol Concepts 2015; 2:199-210. [PMID: 25962029 DOI: 10.1515/bmc.2011.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/01/2011] [Indexed: 01/05/2023] Open
Abstract
Coiled coils are formed by two or more α-helices wrapped around one another. This structural motif often guides di-, tri- or multimerization of proteins involved in diverse biological processes such as membrane fusion, signal transduction and the organization of the cytoskeleton. Although coiled coil motifs seem conceptually simple and their existence was proposed in the early 1950s, the high variability of the motif makes coiled coil prediction from sequence a difficult task. They might be confused with intrinsically disordered sequences and even more with a recently described structural motif, the charged single α-helix. By contrast, the versatility of coiled coil structures renders them an ideal candidate for protein (re)design and many novel variants have been successfully created to date. In this paper, we review coiled coils in the light of protein evolution by putting our present understanding of the motif and its variants in the context of structural interconversions. We argue that coiled coils are ideal subjects for studies of subtle and large-scale structural changes because of their well-characterized and versatile nature.
Collapse
|
12
|
Rabe M, Zope HR, Kros A. Interplay between Lipid Interaction and Homo-coiling of Membrane-Tethered Coiled-Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9953-9964. [PMID: 26302087 DOI: 10.1021/acs.langmuir.5b02094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The designed coiled-coil-forming peptides E [(EIAALEK)3] and K [(KIAALKE)3] are known to trigger efficient membrane fusion when they are tethered to lipid vesicles in the form of lipopeptides. Knowledge of their secondary structure is a key element in understanding their role in membrane fusion. Special conditions can be found at the interface of the membrane, where the peptides are confined in close proximity to other peptide molecules as well as to the lipid interface. Consequently, different structural states were proposed for the peptides when tethered to this interface. Due to the multitude of possible states, determining the structure solely on the basis of circular dichroism (CD) spectra at a single temperature can be misleading. In addition, it has not yet been possible to unambiguously distinguish between the membrane-bound and the coiled-coil states of these peptides by means of infrared (IR) spectroscopy due to their very similar amide I' bands. Here, the molecular basis of this similarity is investigated by means of site-specific (13)C-labeled FTIR spectroscopy. Structural similarities between the membrane-interacting helix of K and the homo-coiled-coil-forming helix of E are shown to cause the similar spectroscopic properties. Furthermore, the peptide structure is investigated using temperature-dependent CD and IR spectroscopy, and it is shown that the different states can be distinguished on the basis of their thermal behavior. It is shown that the two peptides behave fundamentaly differently when tethered to the lipid membrane, which implies that their role during membrane fusion is different and the mechanism of this process is asymmetric.
Collapse
Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Harshal R Zope
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry-Supramolecular and Biomaterial Chemistry, Leiden University , Einsteinweg 55, 2333CC Leiden, The Netherlands
| |
Collapse
|
13
|
Impagliazzo A, Milder F, Kuipers H, Wagner MV, Zhu X, Hoffman RMB, van Meersbergen R, Huizingh J, Wanningen P, Verspuij J, de Man M, Ding Z, Apetri A, Kükrer B, Sneekes-Vriese E, Tomkiewicz D, Laursen NS, Lee PS, Zakrzewska A, Dekking L, Tolboom J, Tettero L, van Meerten S, Yu W, Koudstaal W, Goudsmit J, Ward AB, Meijberg W, Wilson IA, Radošević K. A stable trimeric influenza hemagglutinin stem as a broadly protective immunogen. Science 2015; 349:1301-6. [PMID: 26303961 DOI: 10.1126/science.aac7263] [Citation(s) in RCA: 442] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/29/2015] [Indexed: 12/14/2022]
Abstract
The identification of human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem revitalized hopes of developing a universal influenza vaccine. Using a rational design and library approach, we engineered stable HA stem antigens ("mini-HAs") based on an H1 subtype sequence. Our most advanced candidate exhibits structural and bnAb binding properties comparable to those of full-length HA, completely protects mice in lethal heterologous and heterosubtypic challenge models, and reduces fever after sublethal challenge in cynomolgus monkeys. Antibodies elicited by this mini-HA in mice and nonhuman primates bound a wide range of HAs, competed with human bnAbs for HA stem binding, neutralized H5N1 viruses, and mediated antibody-dependent effector activity. These results represent a proof of concept for the design of HA stem mimics that elicit bnAbs against influenza A group 1 viruses.
Collapse
Affiliation(s)
- Antonietta Impagliazzo
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands.
| | - Fin Milder
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Harmjan Kuipers
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Michelle V Wagner
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ryan M B Hoffman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ruud van Meersbergen
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jeroen Huizingh
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Patrick Wanningen
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Johan Verspuij
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Martijn de Man
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Zhaoqing Ding
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Adrian Apetri
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Başak Kükrer
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Eveline Sneekes-Vriese
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Danuta Tomkiewicz
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Nick S Laursen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter S Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anna Zakrzewska
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Liesbeth Dekking
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jeroen Tolboom
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Lisanne Tettero
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Sander van Meerten
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wouter Koudstaal
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Jaap Goudsmit
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Wim Meijberg
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Katarina Radošević
- Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, Archimedesweg 4-6, 2301 CA Leiden, Netherlands
| |
Collapse
|
14
|
The deconvolution of differential scanning calorimetry unfolding transitions. Methods 2015; 76:78-86. [DOI: 10.1016/j.ymeth.2014.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
|
15
|
Rabe M, Boyle A, Zope HR, Versluis F, Kros A. Determination of oligomeric states of peptide complexes using thermal unfolding curves. Biopolymers 2015; 104:65-72. [DOI: 10.1002/bip.22598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/19/2014] [Accepted: 11/30/2014] [Indexed: 01/18/2023]
Affiliation(s)
- Martin Rabe
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 leiden Netherlands
| | - Aimee Boyle
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 leiden Netherlands
| | - Harshal R. Zope
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 leiden Netherlands
| | - Frank Versluis
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 leiden Netherlands
| | - Alexander Kros
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 leiden Netherlands
| |
Collapse
|
16
|
Hernández-Moreno AV, Perdomo-Abúndez FC, Pérez-Medina Martínez V, Luna-Bárcenas G, Villaseñor-Ortega F, Pérez NO, López-Morales CA, Flores-Ortiz LF, Medina-Rivero E. Structural and functional characterization of a recombinant leucine aminopeptidase. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Cukier RI. Dihedral angle entropy measures for intrinsically disordered proteins. J Phys Chem B 2015; 119:3621-34. [PMID: 25679039 DOI: 10.1021/jp5102412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein stability is based on a delicate balance between energetic and entropic factors. Intrinsically disordered proteins (IDPs) interacting with a folded partner protein in the act of binding can order the IDP to form the correct functional interface by decrease in the overall free energy. In this work, we evaluate the part of the entropic cost of ordering an IDP arising from their dihedral states. The IDP studied is a leucine zipper dimer that we simulate with molecular dynamics and find that it does show disorder in six phi and psi dihedral angles of the N terminal sequence of one monomer. Essential to ascertain is the degree of disorder in the IDP, and we do so by considering the entire, discretized probability distribution function of N dihedrals with M conformers per dihedral. A compositional clustering method is introduced, whereby the NS = N(M) states are formed from the Cartesian product of each dihedral's conformational space. Clustering is carried out with a version of a k-means algorithm that accounts for the circular nature of dihedral angles. For the 12 dihedrals each found to have three conformers, among the resulting 531441 states, their populations show that the first 100 (500) most populated states account for ∼65% (∼90%) of the entire population, indicating that there are strong dependencies among the dihedrals' conformations. These state populations are used to evaluate a Kullback-Leibler divergence entropy measure and obtain the dihedral configurational entropy S. At 300 K, TS ∼ 3 kcal/mol, showing that IDP entropy, while roughly half that would be expected from independently distributed dihedrals, can be a decisive contributor to the free energy of this IDP binding and ordering.
Collapse
Affiliation(s)
- Robert I Cukier
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824-1322, United States
| |
Collapse
|
18
|
Donten ML, Hassan S, Popp A, Halter J, Hauser K, Hamm P. pH-jump induced leucine zipper folding beyond the diffusion limit. J Phys Chem B 2015; 119:1425-32. [PMID: 25536860 DOI: 10.1021/jp511539c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The folding of a pH-sensitive leucine zipper, that is, a GCN4 mutant containing eight glutamic acid residues, has been investigated. A pH-jump induced by a caged proton (o-nitrobenzaldehyde, oNBA) is employed to initiate the process, and time-resolved IR spectroscopy of the amide I band is used to probe it. The experiment has been carefully designed to minimize the buffer capacity of the sample solution so that a large pH jump can be achieved, leading to a transition from a completely unfolded to a completely folded state with a single laser shot. In order to eliminate the otherwise rate-limiting diffusion-controlled step of the association of two peptides, they have been covalently linked. The results for the folding kinetics of the cross-linked peptide are compared with those of an unlinked peptide, which reveals a detailed picture of the folding mechanism. That is, folding occurs in two steps, one on an ∼1-2 μs time scale leading to a partially folded α-helix even in the monomeric case and a second one leading to the final coiled-coil structure on distinctively different time scales of ∼30 μs for the cross-linked peptide and ∼200 μs for the unlinked peptide. By varying the initial pH, it is found that the folding mechanism is consistent with a thermodynamic two-state model, despite the fact that a transient intermediate is observed in the kinetic experiment.
Collapse
Affiliation(s)
- Mateusz L Donten
- Department of Chemistry, Universität Zürich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | | | | | | | | |
Collapse
|
19
|
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
|
20
|
Walavalkar NM, Gordon N, Williams DC. Unique features of the anti-parallel, heterodimeric coiled-coil interaction between methyl-cytosine binding domain 2 (MBD2) homologues and GATA zinc finger domain containing 2A (GATAD2A/p66α). J Biol Chem 2013; 288:3419-27. [PMID: 23239876 PMCID: PMC3561560 DOI: 10.1074/jbc.m112.431346] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/07/2012] [Indexed: 12/30/2022] Open
Abstract
The methyl-cytosine binding domain 2 (MBD2)-nucleosome remodeling and deacetylase (NuRD) complex recognizes methylated DNA and silences expression of associated genes through histone deacetylase and nucleosome remodeling functions. Our previous structural work demonstrated that a coiled-coil interaction between MBD2 and GATA zinc finger domain containing 2A (GATAD2A/p66α) proteins recruits the chromodomain helicase DNA-binding protein (CHD4/Mi2β) to the NuRD complex and is necessary for MBD2-mediated DNA methylation-dependent gene silencing in vivo (Gnanapragasam, M. N., Scarsdale, J. N., Amaya, M. L., Webb, H. D., Desai, M. A., Walavalkar, N. M., Wang, S. Z., Zu Zhu, S., Ginder, G. D., and Williams, D. C., Jr. (2011) p66α-MBD2 coiled-coil interaction and recruitment of Mi-2 are critical for globin gene silencing by the MBD2-NuRD complex. Proc. Natl. Acad. Sci. U.S.A. 108, 7487-7492). The p66α-MBD2 interaction differs from most coiled-coils studied to date by forming an anti-parallel heterodimeric complex between two peptides that are largely monomeric in isolation. To further characterize unique features of this complex that drive heterodimeric specificity and high affinity binding, we carried out biophysical analyses of MBD2 and the related homologues MBD3, MBD3-like protein 1 (MBD3L1), and MBD3-like protein 2 (MBD3L2) as well as specific mutations that modify charge-charge interactions and helical propensity of the coiled-coil domains. Analytical ultracentrifugation analyses show that the individual peptides remain monomeric in isolation even at 300 μM in concentration for MBD2. Circular dichroism analyses demonstrate a direct correlation between helical content of the coiled-coil domains in isolation and binding affinity for p66α. Furthermore, complementary electrostatic surface potentials and inherent helical content of each peptide are necessary to maintain high-affinity association. These factors lead to a binding affinity hierarchy of p66α for the different MBD2 homologues (MBD2 ≈ MBD3 > MBD3L1 ≈ MBD3L2) and suggest a hierarchical regulatory model in tissue and life cycle stage-specific silencing by NuRD complexes.
Collapse
Affiliation(s)
- Ninad M. Walavalkar
- From the Integrative Life Sciences Program
- Department of Pathology and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298 and
| | | | - David C. Williams
- Department of Pathology and the Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298 and
| |
Collapse
|
21
|
Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
Collapse
Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
| | | | | | | | | | | | | | | |
Collapse
|
22
|
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
|
23
|
Davies OR, Maman JD, Pellegrini L. Structural analysis of the human SYCE2-TEX12 complex provides molecular insights into synaptonemal complex assembly. Open Biol 2012; 2:120099. [PMID: 22870393 PMCID: PMC3411106 DOI: 10.1098/rsob.120099] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 06/26/2012] [Indexed: 11/12/2022] Open
Abstract
The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2-TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2-TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC.
Collapse
Affiliation(s)
- Owen R Davies
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK.
| | | | | |
Collapse
|
24
|
Fletcher JM, Boyle AL, Bruning M, Bartlett GJ, Vincent TL, Zaccai NR, Armstrong CT, Bromley EHC, Booth PJ, Brady RL, Thomson AR, Woolfson DN. A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology. ACS Synth Biol 2012; 1:240-50. [PMID: 23651206 DOI: 10.1021/sb300028q] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.
Collapse
Affiliation(s)
- Jordan M. Fletcher
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Aimee L. Boyle
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Marc Bruning
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Thomas L. Vincent
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Nathan R. Zaccai
- School of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
| | - Craig T. Armstrong
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
- School of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
| | | | - Paula J. Booth
- School of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
| | - R. Leo Brady
- School of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
| | - Andrew R. Thomson
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8
1TS, U.K
- School of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
| |
Collapse
|
25
|
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
|
26
|
Constantinescu Aruxandei D, Makbul C, Koturenkiene A, Lüdemann MB, Herrmann C. Dimerization-Induced Folding of MST1 SARAH and the Influence of the Intrinsically Unstructured Inhibitory Domain: Low Thermodynamic Stability of Monomer. Biochemistry 2011; 50:10990-1000. [DOI: 10.1021/bi201110h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Cihan Makbul
- Department of Physical
Chemistry I, Ruhr University Bochum, Universitätsstrasse 150, 44780
Bochum, Germany
| | - Agne Koturenkiene
- Department of Physical
Chemistry I, Ruhr University Bochum, Universitätsstrasse 150, 44780
Bochum, Germany
| | - Maik-Borris Lüdemann
- Department of Physical
Chemistry I, Ruhr University Bochum, Universitätsstrasse 150, 44780
Bochum, Germany
| | - Christian Herrmann
- Department of Physical
Chemistry I, Ruhr University Bochum, Universitätsstrasse 150, 44780
Bochum, Germany
| |
Collapse
|
27
|
Blackwood JK, Rzechorzek NJ, Abrams AS, Maman JD, Pellegrini L, Robinson NP. Structural and functional insights into DNA-end processing by the archaeal HerA helicase-NurA nuclease complex. Nucleic Acids Res 2011; 40:3183-96. [PMID: 22135300 PMCID: PMC3326311 DOI: 10.1093/nar/gkr1157] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Helicase–nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA and NurA must interact in a complex with specific subunit stoichiometry to process DNA ends efficiently. We determine crystallographically that NurA folds in a toroidal dimer of intertwined RNaseH-like domains. The central channel of the NurA dimer is too narrow for double-stranded DNA but appears well suited to accommodate one or two strands of an unwound duplex. We map a critical interface of the complex to an exposed hydrophobic epitope of NurA abutting the active site. Based upon the presented evidence, we propose alternative mechanisms of DNA end processing by the HerA-NurA complex.
Collapse
Affiliation(s)
- John K Blackwood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | | | | | | |
Collapse
|
28
|
Cukier RI. A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper. J Chem Phys 2011; 134:045104. [PMID: 21280805 DOI: 10.1063/1.3548074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] hamiltonian temperature replica exchange method (HTREM), which scales the hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer does not with HTREM_MS, giving confidence in the method. The interface formation time scale is sufficiently short that using HTREM_MS as a screening tool to validate leucine zipper design methods may be feasible.
Collapse
Affiliation(s)
- Robert I Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA.
| |
Collapse
|
29
|
Kapinos LE, Burkhard P, Herrmann H, Aebi U, Strelkov SV. Simultaneous Formation of Right- and Left-handed Anti-parallel Coiled-coil Interfaces by a Coil2 Fragment of Human Lamin A. J Mol Biol 2011; 408:135-46. [DOI: 10.1016/j.jmb.2011.02.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
|
30
|
Craig CJ, Goodman JL, Schepartz A. Enhancing β3 -peptide bundle stability by design. Chembiochem 2011; 12:1035-8. [PMID: 21455925 DOI: 10.1002/cbic.201000753] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/07/2022]
Abstract
We reported recently that certain β(3) -peptides self-assemble in aqueous solution into discrete bundles of unique structure and defined stoichiometry. The first β-peptide bundle reported was the octameric Zwit-1F, whose fold is characterized by a well-packed, leucine-rich core and a salt-bridge-rich surface. Close inspection of the Zwit-1F structure revealed four nonideal interhelical salt-bridge interactions whose heavy atom-heavy atom distances were longer than found in natural proteins of known structure. Here we demonstrate that the thermodynamic stability of a β-peptide bundle can be enhanced by optimizing the length of these four interhelical salt bridges. Combined with previous work on the role of internal packing residues, these results provide another critical step in the "bottom-up" formation of β-peptide assemblies with defined sizes, reproducible structures, and sophisticated function.
Collapse
Affiliation(s)
- Cody J Craig
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
| | | | | |
Collapse
|
31
|
Nevzorov IA, Nikolaeva OP, Kainov YA, Redwood CS, Levitsky DI. Conserved noncanonical residue Gly-126 confers instability to the middle part of the tropomyosin molecule. J Biol Chem 2011; 286:15766-72. [PMID: 21454502 DOI: 10.1074/jbc.m110.209353] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tropomyosin (Tm) is a two-stranded α-helical coiled-coil protein with a well established role in regulation of actin cytoskeleton and muscle contraction. It is believed that many Tm functions are enabled by its flexibility whose nature has not been completely understood. We hypothesized that the well conserved non-canonical residue Gly-126 causes local destabilization of Tm. To test this, we substituted Gly-126 in skeletal muscle α-Tm either with an Ala residue, which should stabilize the Tm α-helix, or with an Arg residue, which is expected to stabilize both α-helix and coiled-coil structure of Tm. We have shown that both mutations dramatically reduce the rate of Tm proteolysis by trypsin at Asp-133. Differential scanning calorimetry was used for detailed investigation of thermal unfolding of the Tm mutants, both free in solution and bound to F-actin. It was shown that a significant part of wild type Tm unfolds in a non-cooperative manner at low temperature, and both mutations confer cooperativity to this part of the Tm molecule. The size of the flexible middle part of Tm is estimated to be 60-70 amino acid residues, about a quarter of the Tm molecule. Thus, our results show that flexibility is unevenly distributed in the Tm molecule and achieves the highest extent in its middle part. We conclude that the highly conserved Gly-126, acting in concert with the previously identified non-canonical Asp-137, destabilizes the middle part of Tm, resulting in a more flexible region that is important for Tm function.
Collapse
Affiliation(s)
- Ilya A Nevzorov
- AN Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | |
Collapse
|
32
|
Carrillo R, Privalov P. Unfolding of bZIP dimers formed by the ATF-2 and c-Jun transcription factors is not a simple two-state transition. Biophys Chem 2010; 151:149-54. [DOI: 10.1016/j.bpc.2010.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/10/2010] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
|
33
|
Farber P, Darmawan H, Sprules T, Mittermaier A. Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy. J Am Chem Soc 2010; 132:6214-22. [PMID: 20377225 DOI: 10.1021/ja100815a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some marginally stable proteins undergo microsecond time scale folding reactions that involve significant populations of partly ordered forms, making it difficult to discern individual steps in their folding pathways. It has been suggested that many of these proteins fold non-cooperatively, with no significant barriers to separate the energy landscape into distinct thermodynamic states. Here we present an approach for studying the cooperativity of rapid protein folding with a combination of differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR) relaxation dispersion experiments, and an analysis of the temperature dependence of amide (1)H and (15)N chemical shifts. We applied this method to the PBX homeodomain (PBX-HD), which folds on the microsecond time scale and produces a broad DSC thermogram with an elevated and steeply sloping native-state heat capacity baseline, making it a candidate for barrierless folding. However, by globally fitting the NMR thermal melt and DSC data, and by comparing these results to those obtained from the NMR relaxation dispersion experiments, we show that the native form of the protein undergoes two-state exchange with a small population of the thermally denatured form, well below the melting temperature. This result directly demonstrates the coexistence of distinct folded and unfolded forms and firmly establishes that folding of PBX-HD is cooperative. Further, we see evidence of large-scale structural and dynamical changes within the native state by NMR, which helps to explain the broad and shallow DSC profile. This study illustrates the potential of combining calorimetry with NMR dynamics experiments to dissect mechanisms of protein folding.
Collapse
Affiliation(s)
- Patrick Farber
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 2K6
| | | | | | | |
Collapse
|
34
|
Salwiczek M, Koksch B. Effects of fluorination on the folding kinetics of a heterodimeric coiled coil. Chembiochem 2010; 10:2867-70. [PMID: 19859931 DOI: 10.1002/cbic.200900518] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mario Salwiczek
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Germany
| | | |
Collapse
|
35
|
Kirwan JP, Hodges RS. Critical interactions in the stability control region of tropomyosin. J Struct Biol 2010; 170:294-306. [PMID: 20144718 DOI: 10.1016/j.jsb.2010.01.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 11/16/2022]
Abstract
Our laboratory has recently described a stability control region in the two-stranded alpha-helical coiled-coil alpha-tropomyosin that accounts for overall protein stability but is not required for folding (Hodges et al., 2009). We have used a synthetic peptide approach to investigate three stability control sites within the stability control region (residues 97-118). Two of the sites, electrostatic cluster 1 (97-104, EELDRAQE) and electrostatic cluster 2 (112-118, KLEEAEK), feature sequences with unusually high charge density and the potential to form multiple intrachain and interchain salt bridges (ionic attractions). A third site (105-111, RLATALQ) features an e position Leu residue, an arrangement known previously to enhance coiled-coil stability modestly. A native peptide and seven peptide analogs of the tropomyosin sequence 85-119 were prepared by Fmoc solid-phase peptide synthesis. Thermal stability measurements by circular dichroism (CD) spectroscopy revealed the following T(m) values for the native peptide and three key analogs: 52.9 degrees C (Native), 46.0 degrees C (R101A), 45.3 degrees C (K112A/K118A), and 27.9 degrees C (L110A). The corresponding DeltaT(m) values for the analogs, relative to the native peptide, are -6.9 degrees C, -7.6 degrees C, and -25.0 degrees C, respectively. The dramatic contribution to stability made by L110e is three times greater than the contribution of either electrostatic cluster 1 or 2, likely resulting from a novel hydrophobic interaction not previously observed. These thermal stability results were corroborated by temperature profiling analyses using reversed-phase high-performance liquid chromatography (RP-HPLC). We believe that the combined contributions of the interactions within the three stability control sites are responsible for the effect of the stability control region in tropomyosin, with the Leu110e contribution being most critical.
Collapse
Affiliation(s)
- J Paul Kirwan
- Program in Structural Biology and Biophysics, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | | |
Collapse
|
36
|
Imamura H, Isogai Y, Takekiyo T, Kato M. Effect of pressure on the secondary structure of coiled coil peptide GCN4-p1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:193-8. [DOI: 10.1016/j.bbapap.2009.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 09/28/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
|
37
|
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
|
38
|
Kazakov AS, Markov DI, Gusev NB, Levitsky DI. Thermally induced structural changes of intrinsically disordered small heat shock protein Hsp22. Biophys Chem 2009; 145:79-85. [DOI: 10.1016/j.bpc.2009.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 08/31/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
|
39
|
Tarafdar PK, Vedantam LV, Kondreddy A, Podile AR, Swamy MJ. Biophysical investigations on the aggregation and thermal unfolding of harpinPss and identification of leucine-zipper-like motifs in harpins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1684-92. [DOI: 10.1016/j.bbapap.2009.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/11/2009] [Accepted: 07/31/2009] [Indexed: 11/17/2022]
|
40
|
Liu Z, Zhang J, Wang X, Ding Y, Wu J, Shi Y. Temperature-induced partially unfolded state of hUBF HMG Box-5: Conformational and dynamic investigations of the Box-5 thermal intermediate ensemble. Proteins 2009; 77:432-47. [DOI: 10.1002/prot.22454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
41
|
Miller M. The importance of being flexible: the case of basic region leucine zipper transcriptional regulators. Curr Protein Pept Sci 2009; 10:244-69. [PMID: 19519454 DOI: 10.2174/138920309788452164] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Large volumes of protein sequence and structure data acquired by proteomic studies led to the development of computational bioinformatic techniques that made possible the functional annotation and structural characterization of proteins based on their primary structure. It has become evident from genome-wide analyses that many proteins in eukaryotic cells are either completely disordered or contain long unstructured regions that are crucial for their biological functions. The content of disorder increases with evolution indicating a possibly important role of disorder in the regulation of cellular systems. Transcription factors are no exception and several proteins of this class have recently been characterized as premolten/molten globules. Yet, mammalian cells rely on these proteins to control expression of their 30,000 or so genes. Basic region:leucine zipper (bZIP) DNA-binding proteins constitute a major class of eukaryotic transcriptional regulators. This review discusses how conformational flexibility "built" into the amino acid sequence allows bZIP proteins to interact with a large number of diverse molecular partners and to accomplish their manifold cellular tasks in a strictly regulated and coordinated manner.
Collapse
Affiliation(s)
- Maria Miller
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA.
| |
Collapse
|
42
|
Cobos ES, Iglesias-Bexiga M, Ruiz-Sanz J, Mateo PL, Luque I, Martinez JC. Thermodynamic Characterization of the Folding Equilibrium of the Human Nedd4-WW4 Domain: At the Frontiers of Cooperative Folding. Biochemistry 2009; 48:8712-20. [DOI: 10.1021/bi9007758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eva S. Cobos
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Manuel Iglesias-Bexiga
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Pedro L. Mateo
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Irene Luque
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Jose C. Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| |
Collapse
|
43
|
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
|
44
|
Armstrong CT, Boyle AL, Bromley EHC, Mahmoud ZN, Smith L, Thomson AR, Woolfson DN. Rational design of peptide-based building blocks for nanoscience and synthetic biology. Faraday Discuss 2009; 143:305-17; discussion 359-72. [DOI: 10.1039/b901610d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
45
|
Abstract
Ultrasensitive microcalorimetric techniques for measuring the heat capacities of proteins in dilute solutions over a broad temperature range (DSC) and the heats of protein reactions at fixed temperatures (ITC) are described and the methods of working with these instruments are considered. Particular attention is paid to analyzing the thermal properties of individual proteins, their stability, the energetics of their folding, and their association with specific macromolecular partners. Use of these calorimetric methods is illustrated with examples of small compact globular proteins, small proteins having loose noncompact structure, multidomain proteins, and protein complexes, particularly with DNA.
Collapse
Affiliation(s)
- Peter L Privalov
- Department of Biology, John Hopkins University, Baltimore, MD, USA
| |
Collapse
|
46
|
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
|
47
|
Probing the functional tolerance of the b subunit of Escherichia coli ATP synthase for sequence manipulation through a chimera approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:583-91. [DOI: 10.1016/j.bbabio.2008.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/05/2008] [Accepted: 03/07/2008] [Indexed: 11/19/2022]
|
48
|
Marsden HR, Korobko AV, van Leeuwen ENM, Pouget EM, Veen SJ, Sommerdijk NAJM, Kros A. Noncovalent Triblock Copolymers Based on a Coiled-Coil Peptide Motif. J Am Chem Soc 2008; 130:9386-93. [DOI: 10.1021/ja800254w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Robson Marsden
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander V. Korobko
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ellen N. M. van Leeuwen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Emilie M. Pouget
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sandra J. Veen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nico A. J. M. Sommerdijk
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander Kros
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
49
|
Liu Y, Chapagain PP, Parra JL, Gerstman BS. Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper. J Chem Phys 2008; 128:045106. [DOI: 10.1063/1.2831513] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
50
|
Balakrishnan G, Hu Y, Case MA, Spiro TG. Microsecond melting of a folding intermediate in a coiled-coil peptide, monitored by T-jump/UV Raman spectroscopy. J Phys Chem B 2007; 110:19877-83. [PMID: 17020373 DOI: 10.1021/jp061987f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A truncated version of the GCN4 coiled-coil peptide has been studied by ultraviolet resonance Raman (UVRR) spectroscopy with 197 nm excitation, where amide modes are optimally enhanced. Although the CD melting curve could be satisfactorily described with a two-state transition having Tm = 30 degrees C, singular value decomposition of the UVRR data yielded three principal components, whose temperature dependence implicates an intermediate form between the folded and unfolded forms, with formation and melting temperatures of 10 and 40 degrees C. Two alpha-helical amide III bands, at 1340 and 1300 cm(-1), melted out selectively at 10 and 40 degrees C, respectively, and are assigned to hydrated and unhydrated helical regions. The hydrated regions are proposed to be melted in the intermediate form, while the unhydrated regions are intact. Time-resolved UVRR spectra following laser-induced temperature jumps revealed two relaxations, with time constants of 0.2 and 15 mus. These are suggested to reflect the melting times of hydrated and unhydrated helices. The unhydrated helical region may be associated with a 14-residue "trigger" sequence that has been identified in the C-terminal half of GCN4. Dehydration of helices may be a key step in the folding of coiled-coils.
Collapse
|