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Woolfson DN. A Brief History of De Novo Protein Design: Minimal, Rational, and Computational. J Mol Biol 2021; 433:167160. [PMID: 34298061 DOI: 10.1016/j.jmb.2021.167160] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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2
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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3
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Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner-Hahn JE, Pecoraro VL. Making or Breaking Metal-Dependent Catalytic Activity: The Role of Stammers in Designed Three-Stranded Coiled Coils. Angew Chem Int Ed Engl 2020; 59:20445-20449. [PMID: 32748510 PMCID: PMC7722090 DOI: 10.1002/anie.202008356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/21/2020] [Indexed: 12/31/2022]
Abstract
While many life-critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three-stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper-catalyzed nitrite reductase activity (CuNiR). In contrast, the well-established zinc-catalyzed carbonic anhydrase activity (p-nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non-coordinating and non-acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | | | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
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Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner‐Hahn JE, Pecoraro VL. Making or Breaking Metal‐Dependent Catalytic Activity: The Role of Stammers in Designed Three‐Stranded Coiled Coils. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Audrey E. Tolbert
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Aniruddha Deb
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
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5
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Hellmund KS, Lospichl B, Böttcher C, Ludwig K, Keiderling U, Noirez L, Weiß A, Mikolajczak DJ, Gradzielski M, Koksch B. Functionalized peptide hydrogels as tunable extracellular matrix mimics for biological applications. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katharina S. Hellmund
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Benjamin Lospichl
- Stranski‐Laboratory of Physical and Theoretical Chemistry Institute of Chemistry, Technische Universität Berlin Berlin Germany
| | - Christoph Böttcher
- Center of Electron Microscopy at Freie Universität Berlin Institute of Chemistry and Biochemistry and CoreFacility BioSupraMol Freie Universität Berlin Berlin Germany
| | - Kai Ludwig
- Center of Electron Microscopy at Freie Universität Berlin Institute of Chemistry and Biochemistry and CoreFacility BioSupraMol Freie Universität Berlin Berlin Germany
| | - Uwe Keiderling
- Department Experiment Control and Data Acquisition Helmholtz‐Zentrum Berlin für Materialien und Energie Berlin Germany
| | - Laurence Noirez
- Laboratoire Léon Brillouin (CEA‐CNRS) Université Paris‐Saclay Gif‐sur‐Yvette Cédex France
| | - Annika Weiß
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Dorian J. Mikolajczak
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
| | - Michael Gradzielski
- Stranski‐Laboratory of Physical and Theoretical Chemistry Institute of Chemistry, Technische Universität Berlin Berlin Germany
| | - Beate Koksch
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin Berlin Germany
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6
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Naturally Acquired Antibody Responses to a Synthetic Malaria Antigen AS202.11. J Trop Med 2017; 2017:6843701. [PMID: 29138641 PMCID: PMC5613363 DOI: 10.1155/2017/6843701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/07/2017] [Indexed: 11/20/2022] Open
Abstract
Background A major challenge to malaria vaccine development is identification of protective epitopes and respective protective immune responses. Objective To characterize naturally acquired Immunoglobulin G (IgG) responses to the synthetic peptide AS202.11, a malaria vaccine candidate. Methodology This community based cross-sectional study enrolled 320 participants aged 1 year and above. Demographic information was recorded through interviews. Detection of P. falciparum infection was done by microscopy, malaria rapid diagnostic test, and polymerase chain reaction. ELISA was used to detect IgG antibody. Data was analyzed using STATA. Results The overall AS202.11 IgG seropositivity was 78.8% (73.9–82.9). Seropositivity by age categories was ≤12 years [74.3% (67.4–80.2)], 13–40 years [85.3% (76.5–91.1)], and >40 years [82.6% (68.7–91.1)]. Compared to the ≤ 12-year-old group, aORs for the other groups were 2.22 (1.14–4.32), p = 0.019, and 1.87 (0.81–4.35), p = 0.143, for the 13–40-year-old and >40-year-old groups, respectively. The 13–40-year-old group had more seropositive individuals compared to the ≤ 12-year-old group. Conclusion We report a high degree of recognition of AS202.11 by IgG elicited by field P. falciparum strains, suggesting its close similarity to native P. falciparum antigens and possible suitability of the peptide as a future malaria vaccine candidate.
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Negahdaripour M, Golkar N, Hajighahramani N, Kianpour S, Nezafat N, Ghasemi Y. Harnessing self-assembled peptide nanoparticles in epitope vaccine design. Biotechnol Adv 2017; 35:575-596. [PMID: 28522213 PMCID: PMC7127164 DOI: 10.1016/j.biotechadv.2017.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/23/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Vaccination has been one of the most successful breakthroughs in medical history. In recent years, epitope-based subunit vaccines have been introduced as a safer alternative to traditional vaccines. However, they suffer from limited immunogenicity. Nanotechnology has shown value in solving this issue. Different kinds of nanovaccines have been employed, among which virus-like nanoparticles (VLPs) and self-assembled peptide nanoparticles (SAPNs) seem very promising. Recently, SAPNs have attracted special interest due to their unique properties, including molecular specificity, biodegradability, and biocompatibility. They also resemble pathogens in terms of their size. Their multivalency allows an orderly repetitive display of antigens on their surface, which induces a stronger immune response than single immunogens. In vaccine design, SAPN self-adjuvanticity is regarded an outstanding advantage, since the use of toxic adjuvants is no longer required. SAPNs are usually composed of helical or β-sheet secondary structures and are tailored from natural peptides or de novo structures. Flexibility in subunit selection opens the door to a wide variety of molecules with different characteristics. SAPN engineering is an emerging area, and more novel structures are expected to be generated in the future, particularly with the rapid progress in related computational tools. The aim of this review is to provide a state-of-the-art overview of self-assembled peptide nanoparticles and their use in vaccine design in recent studies. Additionally, principles for their design and the application of computational approaches to vaccine design are summarized.
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Affiliation(s)
- Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Golkar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutics Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nasim Hajighahramani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sedigheh Kianpour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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8
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Cangelosi V, Ruckthong L, Pecoraro VL. Lead(II) Binding in Natural and Artificial Proteins. Met Ions Life Sci 2017; 17:/books/9783110434330/9783110434330-010/9783110434330-010.xml. [PMID: 28731303 PMCID: PMC5771651 DOI: 10.1515/9783110434330-010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This article describes recent attempts to understand the biological chemistry of lead using a synthetic biology approach. Lead binds to a variety of different biomolecules ranging from enzymes to regulatory and signaling proteins to bone matrix. We have focused on the interactions of this element in thiolate-rich sites that are found in metalloregulatory proteins such as Pbr, Znt, and CadC and in enzymes such as δ-aminolevulinic acid dehydratase (ALAD). In these proteins, Pb(II) is often found as a homoleptic and hemidirectic Pb(II)(SR)3- complex. Using first principles of biophysics, we have developed relatively short peptides that can associate into three-stranded coiled coils (3SCCs), in which a cysteine group is incorporated into the hydrophobic core to generate a (cysteine)3 binding site. We describe how lead may be sequestered into these sites, the characteristic spectral features may be observed for such systems and we provide crystallographic insight on metal binding. The Pb(II)(SR)3- that is revealed within these α-helical assemblies forms a trigonal pyramidal structure (having an endo orientation) with distinct conformations than are also found in natural proteins (having an exo conformation). This structural insight, combined with 207Pb NMR spectroscopy, suggests that while Pb(II) prefers hemidirected Pb(II)(SR)3- scaffolds regardless of the protein fold, the way this is achieved within α-helical systems is different than in β-sheet or loop regions of proteins. These interactions between metal coordination preference and protein structural preference undoubtedly are exploited in natural systems to allow for protein conformation changes that define function. Thus, using a design approach that separates the numerous factors that lead to stable natural proteins allows us to extract fundamental concepts on how metals behave in biological systems.
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9
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Murschel F, Fortier C, Jolicoeur M, Hodges RS, De Crescenzo G. Two Complementary Approaches for the Controlled Release of Biomolecules Immobilized via Coiled-Coil Interactions: Peptide Core Mutations and Multivalent Presentation. Biomacromolecules 2017; 18:965-975. [DOI: 10.1021/acs.biomac.6b01830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Frederic Murschel
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Charles Fortier
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Mario Jolicoeur
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Robert S. Hodges
- Department
of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Gregory De Crescenzo
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
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10
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Li C, Ching Han Chang C, Nagel J, Porebski BT, Hayashida M, Akutsu T, Song J, Buckle AM. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform 2016; 17:270-82. [PMID: 26177815 PMCID: PMC6078162 DOI: 10.1093/bib/bbv047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a fundamental role in subcellular infrastructure and controlling trafficking of eukaryotic cells. Given the importance of coiled-coils, multiple bioinformatics tools have been developed to facilitate the systematic and high-throughput prediction of CCDs in proteins. In this article, we review and compare 12 sequence-based bioinformatics approaches and tools for coiled-coil prediction. These approaches can be categorized into two classes: coiled-coil detection and coiled-coil oligomeric state prediction. We evaluated and compared these methods in terms of their input/output, algorithm, prediction performance, validation methods and software utility. All the independent testing data sets are available at http://lightning.med.monash.edu/coiledcoil/. In addition, we conducted a case study of nine human polyglutamine (PolyQ) disease-related proteins and predicted CCDs and oligomeric states using various predictors. Prediction results for CCDs were highly variable among different predictors. Only two peptides from two proteins were confirmed to be CCDs by majority voting. Both domains were predicted to form dimeric coiled-coils using oligomeric state prediction. We anticipate that this comprehensive analysis will be an insightful resource for structural biologists with limited prior experience in bioinformatics tools, and for bioinformaticians who are interested in designing novel approaches for coiled-coil and its oligomeric state prediction.
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11
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Adu B, Cherif MK, Bosomprah S, Diarra A, Arthur FKN, Dickson EK, Corradin G, Cavanagh DR, Theisen M, Sirima SB, Nebie I, Dodoo D. Antibody levels against GLURP R2, MSP1 block 2 hybrid and AS202.11 and the risk of malaria in children living in hyperendemic (Burkina Faso) and hypo-endemic (Ghana) areas. Malar J 2016; 15:123. [PMID: 26921176 PMCID: PMC4769494 DOI: 10.1186/s12936-016-1146-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 02/04/2016] [Indexed: 12/31/2022] Open
Abstract
Background
Differences in parasite transmission intensity influence the process of acquisition of host immunity to Plasmodium falciparum malaria and ultimately, the rate of malaria related morbidity and mortality. Potential vaccines being designed to complement current intervention efforts therefore need to be evaluated against different malaria endemicity backgrounds. Methods The associations between antibody responses to the chimeric merozoite surface protein 1 block 2 hybrid (MSP1 hybrid), glutamate-rich protein region 2 (GLURP R2) and the peptide AS202.11, and the risk of malaria were assessed in children living in malaria hyperendemic (Burkina Faso, n = 354) and hypo-endemic (Ghana, n = 209) areas. Using the same reagent lots and standardized protocols for both study sites, immunoglobulin (Ig) M, IgG and IgG sub-class levels to each antigen were measured by ELISA in plasma from the children (aged 6–72 months). Associations between antibody levels and risk of malaria were assessed using Cox regression models adjusting for covariates. Results There was a significant association between GLURP R2 IgG3 and reduced risk of malaria after adjusting age of children in both the Burkinabe (hazard ratio 0.82; 95 % CI 0.74–0.91, p < 0.0001) and the Ghanaian (HR 0.48; 95 % CI 0.25–0.91, p = 0.02) cohorts. MSP1 hybrid IgM was associated (HR 0.85; 95 % CI 0.73–0.98, p = 0.02) with reduced risk of malaria in Burkina Faso cohort while IgG against AS202.11 in the Ghanaian children was associated with increased risk of malaria (HR 1.29; 95 % CI 1.01–1.65, p = 0.04). Conclusion These findings support further development of GLURP R2 and MSP1 block 2 hybrid, perhaps as a fusion vaccine antigen targeting malaria blood stage that can be deployed in areas of varying transmission intensity. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1146-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
| | - Mariama K Cherif
- Polytechnic University of BoboDioulasso, Bobo-Dioulasso, Burkina Faso. .,Centre National de Recherche et de Formation sur le paludisme, Ouagadougou, Burkina Faso.
| | | | - Amidou Diarra
- Centre National de Recherche et de Formation sur le paludisme, Ouagadougou, Burkina Faso.
| | - Fareed K N Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
| | - Emmanuel K Dickson
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
| | | | - David R Cavanagh
- Institute of Cell, Animal and Population Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le paludisme, Ouagadougou, Burkina Faso.
| | - Issa Nebie
- Centre National de Recherche et de Formation sur le paludisme, Ouagadougou, Burkina Faso.
| | - Daniel Dodoo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.
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12
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Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties. Sci Rep 2015; 5:14063. [PMID: 26370878 PMCID: PMC4570195 DOI: 10.1038/srep14063] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Coiled coils with defined assembly properties and dissociation constants are highly attractive components in synthetic biology and for fabrication of peptide-based hybrid nanomaterials and nanostructures. Complex assemblies based on multiple different peptides typically require orthogonal peptides obtained by negative design. Negative design does not necessarily exclude formation of undesired species and may eventually compromise the stability of the desired coiled coils. This work describe a set of four promiscuous 28-residue de novo designed peptides that heterodimerize and fold into parallel coiled coils. The peptides are non-orthogonal and can form four different heterodimers albeit with large differences in affinities. The peptides display dissociation constants for dimerization spanning from the micromolar to the picomolar range. The significant differences in affinities for dimerization make the peptides prone to thermodynamic social self-sorting as shown by thermal unfolding and fluorescence experiments, and confirmed by simulations. The peptides self-sort with high fidelity to form the two coiled coils with the highest and lowest affinities for heterodimerization. The possibility to exploit self-sorting of mutually complementary peptides could hence be a viable approach to guide the assembly of higher order architectures and a powerful strategy for fabrication of dynamic and tuneable nanostructured materials.
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13
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Hierarchical cascades of instability govern the mechanics of coiled coils: helix unfolding precedes coil unzipping. Biophys J 2015; 107:477-484. [PMID: 25028889 DOI: 10.1016/j.bpj.2014.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/13/2014] [Accepted: 06/03/2014] [Indexed: 12/31/2022] Open
Abstract
Coiled coils are a fundamental emergent motif in proteins found in structural biomaterials, consisting of α-helical secondary structures wrapped in a supercoil. A fundamental question regarding the thermal and mechanical stability of coiled coils in extreme environments is the sequence of events leading to the disassembly of individual oligomers from the universal coiled-coil motifs. To shed light on this phenomenon, here we report atomistic simulations of a trimeric coiled coil in an explicit water solvent and investigate the mechanisms underlying helix unfolding and coil unzipping in the assembly. We employ advanced sampling techniques involving steered molecular dynamics and metadynamics simulations to obtain the free-energy landscapes of single-strand unfolding and unzipping in a three-stranded assembly. Our comparative analysis of the free-energy landscapes of instability pathways shows that coil unzipping is a sequential process involving multiple intermediates. At each intermediate state, one heptad repeat of the coiled coil first unfolds and then unzips due to the loss of contacts with the hydrophobic core. This observation suggests that helix unfolding facilitates the initiation of coiled-coil disassembly, which is confirmed by our 2D metadynamics simulations showing that unzipping of one strand requires less energy in the unfolded state compared with the folded state. Our results explain recent experimental findings and lay the groundwork for studying the hierarchical molecular mechanisms that underpin the thermomechanical stability/instability of coiled coils and similar protein assemblies.
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14
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Zacco E, Anish C, Martin CE, v. Berlepsch H, Brandenburg E, Seeberger PH, Koksch B. A Self-Assembling Peptide Scaffold for the Multivalent Presentation of Antigens. Biomacromolecules 2015; 16:2188-97. [DOI: 10.1021/acs.biomac.5b00572] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Elsa Zacco
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Chakkumkal Anish
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Bacterial Vaccines Discovery and Early Development, Janssen Pharmaceuticals (Johnson & Johnson), Leiden, The Netherlands
| | - Christopher E. Martin
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Hans v. Berlepsch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Research
Center of Electron Microscopy and Core Facility BioSupraMol, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße
36a, 14195 Berlin, Germany
| | - Enrico Brandenburg
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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15
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Plegaria JS, Dzul SP, Zuiderweg ERP, Stemmler TL, Pecoraro VL. Apoprotein Structure and Metal Binding Characterization of a de Novo Designed Peptide, α3DIV, that Sequesters Toxic Heavy Metals. Biochemistry 2015; 54:2858-73. [PMID: 25790102 DOI: 10.1021/acs.biochem.5b00064] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
De novo protein design is a biologically relevant approach that provides a novel process in elucidating protein folding and modeling the metal centers of metalloproteins in a completely unrelated or simplified fold. An integral step in de novo protein design is the establishment of a well-folded scaffold with one conformation, which is a fundamental characteristic of many native proteins. Here, we report the NMR solution structure of apo α3DIV at pH 7.0, a de novo designed three-helix bundle peptide containing a triscysteine motif (Cys18, Cys28, and Cys67) that binds toxic heavy metals. The structure comprises 1067 NOE restraints derived from multinuclear multidimensional NOESY, as well as 138 dihedral angles (ψ, φ, and χ1). The backbone and heavy atoms of the 20 lowest energy structures have a root mean square deviation from the mean structure of 0.79 (0.16) Å and 1.31 (0.15) Å, respectively. When compared to the parent structure α3D, the substitution of Leu residues to Cys enhanced the α-helical content of α3DIV while maintaining the same overall topology and fold. In addition, solution studies on the metalated species illustrated metal-induced stability. An increase in the melting temperatures was observed for Hg(II), Pb(II), or Cd(II) bound α3DIV by 18-24 °C compared to its apo counterpart. Further, the extended X-ray absorption fine structure analysis on Hg(II)-α3DIV produced an average Hg(II)-S bond length at 2.36 Å, indicating a trigonal T-shaped coordination environment. Overall, the structure of apo α3DIV reveals an asymmetric distorted triscysteine metal binding site, which offers a model for native metalloregulatory proteins with thiol-rich ligands that function in regulating toxic heavy metals, such as ArsR, CadC, MerR, and PbrR.
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Affiliation(s)
| | - Stephen P Dzul
- #Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | | | - Timothy L Stemmler
- #Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
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16
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Treviño MA, García-Mayoral MF, Jiménez MÁ, Bastolla U, Bruix M. Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1808-19. [PMID: 25091198 DOI: 10.1016/j.bbapap.2014.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/17/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023]
Abstract
Human centrosomal proteins show a significant, 3.5 fold, bias to be both unstructured and coiled-coils with respect to generic human proteins, based on results from state of the art bioinformatics tools. We hypothesize that this bias means that these proteins adopt an ensemble of disordered and partially helical conformations, with the latter becoming stabilized when these proteins form complexes. Characterization of the structural properties of 13 peptides from 10 different centrosomal proteins ranging in size from 20 to 61 residues by biophysical methods led us to confirm our hypothesis in most cases. Interestingly, the secondary structure adopted by most of these peptides becomes stabilized at acidic pH and it is concentration dependent. For two of them, PIK3R1(453-513) and BRCA1(1253-1273), we observed not only the stabilization of helical structure through self-association, but also the presence of β-structures linked to the formation of high molecular weight oligomers. These oligomers are the predominant forms detected by CD, but unobservable by liquid state NMR. BRCA1(1397-1424) and MAP3K11(396-441) populate helical structures that can also self-associate at pH3 through oligomeric species. Four peptides, derived from three proteins, namely CCNA2(103-123), BRCA1(1253-1273), BRCA1(1397-1424) and PIK3R1(453-513), can form intermolecular associations that are concomitant with alpha or beta structure stabilization. The self-phosphorylation previously described for the kinase NEK2 did not lead to any stabilization in the peptide's structure of NEK2(303-333), NEK2(341-361), and NEK2(410-430). Based on these results, obtained from a series of peptides derived from a significant number of different centrosomal proteins, we propose that conformational polymorphism, modulated by intermolecular interactions is a general property of centrosomal proteins.
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Affiliation(s)
- Miguel A Treviño
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
| | | | - M Ángeles Jiménez
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
| | - Ugo Bastolla
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Cantoblanco, Madrid, Spain.
| | - Marta Bruix
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain.
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17
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Kirwan JP, Hodges RS. Transmission of stability information through the N-domain of tropomyosin is interrupted by a stabilizing mutation (A109L) in the hydrophobic core of the stability control region (residues 97-118). J Biol Chem 2013; 289:4356-66. [PMID: 24362038 PMCID: PMC3924298 DOI: 10.1074/jbc.m113.507236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tropomyosin (Tm) is an actin-binding, thin filament, two-stranded α-helical coiled-coil critical for muscle contraction and cytoskeletal function. We made the first identification of a stability control region (SCR), residues 97-118, in the Tm sequence that controls overall protein stability but is not required for folding. We also showed that the individual α-helical strands of the coiled-coil are stabilized by Leu-110, whereas the hydrophobic core is destabilized in the SCR by Ala residues at three consecutive d positions. Our hypothesis is that the stabilization of the individual α-helices provides an optimum stability and allows functionally beneficial dynamic motion between the α-helices that is critical for the transmission of stabilizing information along the coiled-coil from the SCR. We prepared three recombinant (rat) Tm(1-131) proteins, including the wild type sequence, a destabilizing mutation L110A, and a stabilizing mutation A109L. These proteins were evaluated by circular dichroism (CD) and differential scanning calorimetry. The single mutation L110A destabilizes the entire Tm(1-131) molecule, showing that the effect of this mutation is transmitted 165 Å along the coiled-coil in the N-terminal direction. The single mutation A109L prevents the SCR from transmitting stabilizing information and separates the coiled-coil into two domains, one that is ∼9 °C more stable than wild type and one that is ∼16 °C less stable. We know of no other example of the substitution of a stabilizing Leu residue in a coiled-coil hydrophobic core position d that causes this dramatic effect. We demonstrate the importance of the SCR in controlling and transmitting the stability signal along this rodlike molecule.
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Affiliation(s)
- J Paul Kirwan
- From the Program in Structural Biology and Biophysics, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045
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18
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Zastrow ML, Pecoraro VL. Designing functional metalloproteins: from structural to catalytic metal sites. Coord Chem Rev 2013; 257:2565-2588. [PMID: 23997273 PMCID: PMC3756834 DOI: 10.1016/j.ccr.2013.02.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.
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Affiliation(s)
- Melissa L. Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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19
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20
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Abstract
Hybrid biomaterials are systems created from components of at least two distinct classes of molecules, for example, synthetic macromolecules and proteins or peptide domains. The synergistic combination of two types of structures may produce new materials that possess unprecedented levels of structural organization and novel properties. This Review focuses on biorecognition-driven self-assembly of hybrid macromolecules into functional hydrogel biomaterials. First, basic rules that govern the secondary structure of peptides are discussed, and then approaches to the specific design of hybrid systems with tailor-made properties are evaluated, followed by a discussion on the similarity of design principles of biomaterials and macromolecular therapeutics. Finally, the future of the field is briefly outlined.
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Affiliation(s)
- Jindřich Kopeček
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
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21
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Kopeček J, Yang J. “Intelligente” Biomaterialien durch Selbstorganisation von Hybridhydrogelen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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22
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Wilger DJ, Bettis SE, Materese CK, Minakova M, Papoian GA, Papanikolas JM, Waters ML. Tunable Energy Transfer Rates via Control of Primary, Secondary, and Tertiary Structure of a Coiled Coil Peptide Scaffold. Inorg Chem 2012; 51:11324-38. [DOI: 10.1021/ic300669t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dale J. Wilger
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Stephanie E. Bettis
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Christopher K. Materese
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Maria Minakova
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Garegin A. Papoian
- Department of Chemistry and
Biochemistry, University of Maryland, College
Park, Maryland 20742, United States
| | - John M. Papanikolas
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department
of Chemistry, CB
3290, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
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23
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Pechar M, Pola R. The coiled coil motif in polymer drug delivery systems. Biotechnol Adv 2012; 31:90-6. [PMID: 22266376 DOI: 10.1016/j.biotechadv.2012.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 12/15/2011] [Accepted: 01/04/2012] [Indexed: 01/23/2023]
Abstract
The coiled coil is a superhelical structural protein motif that has been thoroughly investigated in recent years. Because of the relatively well-understood principles that determine the properties of coiled coil peptides and proteins, macromolecular systems containing the coiled coil motif have been suggested for various applications. This short review focuses on hybrid polymer coiled coil systems designed for drug delivery purposes. After a short introduction, the most important features of the coiled coils (stability, association number, oligomerization selectivity and orientation of helices) are described, and the factors influencing these characteristics are discussed. Several examples of the most interesting biomedical applications of the polymer-coiled coil systems (according to the authors' opinion) are presented.
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Affiliation(s)
- Michal Pechar
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 162 06, Prague 6, Czech Republic.
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24
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Conformational consequences of cooperative binding of a coiled-coil peptide motif to poly(N-(2-hydroxypropyl) methacrylamide) HPMA copolymers. J Control Release 2011; 153:173-9. [DOI: 10.1016/j.jconrel.2011.03.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/07/2011] [Accepted: 03/25/2011] [Indexed: 11/17/2022]
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25
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Apostolovic B, Deacon SPE, Duncan R, Klok HA. Cell uptake and trafficking behavior of non-covalent, coiled-coil based polymer-drug conjugates. Macromol Rapid Commun 2010; 32:11-8. [PMID: 21432965 DOI: 10.1002/marc.201000434] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Indexed: 01/14/2023]
Abstract
This paper reports on the cell uptake and trafficking properties of a series of non-covalent polymer-drug conjugates. These nanomedicines are composed of a poly(N-(2-hydroxypropyl)methacrylamide) backbone functionalized with multiple copies of a drug. The drug moieties are attached to the polymer via a non-covalent, so called coiled coil motif, which is formed by heterodimerization of two complementary peptide strands, one of which is attached to the polymer carrier and the other to the drug. Cytotoxicity and FACS experiments, which were carried out with model anticancer drug or fluorophore conjugates, provided insight into the cell uptake and trafficking behavior of these conjugates.
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Affiliation(s)
- Bojana Apostolovic
- École Polytechnique Fédérale de Lausanne, Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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26
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Zaytsev DV, Xie F, Mukherjee M, Bludin A, Demeler B, Breece RM, Tierney DL, Ogawa MY. Nanometer to millimeter scale peptide-porphyrin materials. Biomacromolecules 2010; 11:2602-9. [PMID: 20804210 PMCID: PMC2952671 DOI: 10.1021/bm100540t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AQ-Pal14 is a 30-residue polypeptide that was designed to form an α-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal14)(2) species that creates two coiled-coil oligomerization domains coordinated to opposite faces of the porphyrin ring. It is found that this species undergoes a buffer-dependent self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like materials were prepared when the reaction was performed in phosphate buffer (20 mM, pH 7). It is suggested that assembly of the globular material is dictated by the conformational properties of the coiled-coil forming AQ-Pal14 peptide, whereas that of the rod-like material involves interactions between Co-PPIX and phosphate ion.
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Affiliation(s)
- Daniil V. Zaytsev
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Fei Xie
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Madmuhita Mukherjee
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Alexey Bludin
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
| | - Borries Demeler
- Center for Analytical Ultracentrifugation of Macromolecular Assemblies, University of Texas Health Science Center, San Antonio, TX 78229
| | - Robert M. Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403
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27
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Cloning and expression of 21.1-kDa tegumental protein of Clonorchis sinensis and human antibody response to it as a trematode–nematode pan-specific serodiagnosis antigen. Parasitol Res 2010; 108:161-8. [DOI: 10.1007/s00436-010-2050-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
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28
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Adi-Harel S, Erlich S, Schmukler E, Cohen-Kedar S, Segev O, Mizrachy L, Hirsch JA, Pinkas-Kramarski R. Beclin 1 self-association is independent of autophagy induction by amino acid deprivation and rapamycin treatment. J Cell Biochem 2010; 110:1262-71. [DOI: 10.1002/jcb.22642] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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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.
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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
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30
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Apostolovic B, Danial M, Klok HA. Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials. Chem Soc Rev 2010; 39:3541-75. [DOI: 10.1039/b914339b] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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31
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Shiga D, Nakane D, Inomata T, Masuda H, Oda M, Noda M, Uchiyama S, Fukui K, Takano Y, Nakamura H, Mizuno T, Tanaka T. The effect of the side chain length of Asp and Glu on coordination structure of Cu(2+) in a de novo designed protein. Biopolymers 2009; 91:907-16. [PMID: 19598226 DOI: 10.1002/bip.21277] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Metal ions in proteins are important not only for the formation of the proper structures but also for various biological activities. For biological functions such as hydrolysis and oxidation, metal ions often adopt unusual coordination structures. We constructed a stable scaffold for metal binding to create distorted metal coordination structures. A stable four stranded alpha-helical coiled-coil structure was used as the scaffold, and the metal binding site was in the cavity created at the center of the structure. Two His residues and one Asp or Glu residue were used to coordinate the metal ions, AM2D and AM2E, respectively. Cu(2+) bound to AM2D with an equatorial planar coordination structure with two His, one Asp, and H(2)O as detected by electron spin resonance and UV spectral analyzes. On the other hand, Cu(2+) had a slightly distorted square planar structure when it bound two His and Glu in AM2E, due to the longer side-chain of the Glu residue as compared to the Asp residue. Computational analysis also supported the distorted coordination structure of Cu(2+) in AM2E. This construct should be useful to create various coordinations of metal ions for catalytic functions.
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Affiliation(s)
- Daigo Shiga
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan
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32
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Hartmann L, Börner HG. Precision polymers: monodisperse, monomer-sequence-defined segments to target future demands of polymers in medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2009; 21:3425-3431. [PMID: 20882508 DOI: 10.1002/adma.200801884] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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33
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Marsh ENG, Buer BC, Ramamoorthy A. Fluorine--a new element in the design of membrane-active peptides. MOLECULAR BIOSYSTEMS 2009; 5:1143-7. [PMID: 19756303 DOI: 10.1039/b909864j] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antimicrobial peptides (also known as genetically encoded peptide antibiotics) are a diverse class of short cationic amphipathic polypeptides that exhibit a broad-spectrum of antimicrobial activities by selectively disrupting the bacterial cell membrane. In this review article, we present the use of fluorinated amino acids in the design of antimicrobial peptides and other membrane-active peptides.
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Affiliation(s)
- E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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34
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Łuczkowski M, Stachura M, Schirf V, Demeler B, Hemmingsen L, Pecoraro VL. Design of thiolate rich metal binding sites within a peptidic framework. Inorg Chem 2009; 47:10875-88. [PMID: 18959366 DOI: 10.1021/ic8009817] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A de novo protein design strategy provides a powerful tool to elucidate how heavy metals interact with proteins.Cysteine derivatives of the TRI peptide family (Ac-G(LKALEEK)4G-NH2) have been shown to bind heavy metals in an unusual trigonal geometry. Our present objective was to design binding sites in R-helical scaffolds that are able to form higher coordination number complexes with Cd(II) and Hg(II). Herein, we evaluate the binding of Cd(II) and Hg(II) to double cysteine substituted TRI peptides lacking intervening leucines between sulfurs in the heptads. We compare a -Cysd-X-X-X-Cysa- binding motif found in TRIL12CL16C to the more common -Cysa-X-X-Cysd- sequence of native proteins found in TRIL9CL12C. Compared to TRI, these substitutions destabilize the helical aggregates,leading to mixtures of two- and three-stranded bundles. The three-stranded coiled coils are stabilized by the addition of metals. TRIL9CL12C forms distorted tetrahedral complexes with both Cd(II) and Hg(II), as supported by UV-vis,CD, 113Cd NMR, 199Hg NMR and 111mCd PAC spectroscopy. Additionally, these signatures are very similar to those found for heavy metal substituted rubredoxin. These results suggest that in terms of Hg(II) binding, TRIL9CL12Ccan be considered as a good mimic of the metallochaperone HAH1, that has previously been shown to form protein dimers. TRIL12CL16C has limited ability to generate homoleptic tetrahedral complexes (Cd(SR)42-). These type of complexes were identified only for Hg(II). However, the spectroscopic signatures suggest a different geometry around the metal ion, demonstrating that effective metal sequestration into the hydrophobic interior of the bundle requires more than simply adding two sulfur residues in adjacent layers of the peptide core. Thus, proper design of metal binding sites must also consider the orientation of cysteine sidechains in a vs d positions of the heptads.
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Affiliation(s)
- Marek Łuczkowski
- Department of Chemistry, UniVersity of Michigan, Ann Arbor, Michigan 48109-1055, USA
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35
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Apostolovic B, Klok HA. pH-Sensitivity of the E3/K3 Heterodimeric Coiled Coil. Biomacromolecules 2008; 9:3173-80. [DOI: 10.1021/bm800746e] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bojana Apostolovic
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, Laboratoire des Polymères Bâtiment MXD, Station 12, 1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, Laboratoire des Polymères Bâtiment MXD, Station 12, 1015 Lausanne, Switzerland
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36
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Mukherjee M, Zhu X, Ogawa MY. Cd2+-Induced Conformational Change of a Synthetic Metallopeptide: Slow Metal Binding Followed by a Slower Conformational Change. Inorg Chem 2008; 47:4430-2. [DOI: 10.1021/ic702370k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madhumita Mukherjee
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Xianchun Zhu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
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Agak GW, Bejon P, Fegan G, Gicheru N, Villard V, Kajava AV, Marsh K, Corradin G. Longitudinal analyses of immune responses to Plasmodium falciparum derived peptides corresponding to novel blood stage antigens in coastal Kenya. Vaccine 2008; 26:1963-71. [PMID: 18342997 DOI: 10.1016/j.vaccine.2008.02.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 01/21/2008] [Accepted: 02/07/2008] [Indexed: 11/29/2022]
Abstract
We have recently described 95 predicted alpha-helical coiled-coil peptides derived from putative Plasmodium falciparum erythrocytic stage proteins. Seventy peptides recognized with the highest level of prevalence by sera from three endemic areas were selected for further studies. In this study, we sequentially examined antibody responses to these synthetic peptides in two cohorts of children at risk of clinical malaria in Kilifi district in coastal Kenya, in order to characterize the level of peptide recognition by age, and the role of anti-peptide antibodies in protection from clinical malaria. Antibody levels from 268 children in the first cohort (Chonyi) were assayed against 70 peptides. Thirty-nine peptides were selected for further study in a second cohort (Junju). The rationale for the second cohort was to confirm those peptides identified as protective in the first cohort. The Junju cohort comprised of children aged 1-6 years old (inclusive). Children were actively followed up to identify episodes of febrile malaria in both cohorts. Of the 70 peptides examined, 32 showed significantly (p<0.05) increased antibody recognition in older children and 40 showed significantly increased antibody recognition in parasitaemic children. Ten peptides were associated with a significantly reduced odds ratio (OR) for an episode of clinical malaria in the first cohort of children and two of these peptides (LR146 and AS202.11) were associated with a significantly reduced OR in both cohorts. LR146 is derived from hypothetical protein PFB0145c in PlasmoDB. Previous work has identified this protein as a target of antibodies effective in antibody dependent cellular inhibition (ADCI). The current study substantiates further the potential of protein PFB0145c and also identifies protein PF11_0424 as another likely target of protective antibodies against P. falciparum malaria.
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Affiliation(s)
- George W Agak
- Department of Biochemistry, University of Lausanne, Chemin des Boveresses 155, 1066-Epalinges, Switzerland
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Tsurkan MV, Ogawa MY. Formation of Peptide Nanospheres and Nanofibrils by Metal Coordination. Biomacromolecules 2007; 8:3908-13. [DOI: 10.1021/bm700879t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikhail V. Tsurkan
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Michael Y. Ogawa
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403
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Villard V, Agak GW, Frank G, Jafarshad A, Servis C, Nébié I, Sirima SB, Felger I, Arevalo-Herrera M, Herrera S, Heitz F, Bäcker V, Druilhe P, Kajava AV, Corradin G. Rapid identification of malaria vaccine candidates based on alpha-helical coiled coil protein motif. PLoS One 2007; 2:e645. [PMID: 17653272 PMCID: PMC1920550 DOI: 10.1371/journal.pone.0000645] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 06/15/2007] [Indexed: 11/18/2022] Open
Abstract
To identify malaria antigens for vaccine development, we selected alpha-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. The corresponding synthetic peptides are expected to mimic structurally "native" epitopes. Indeed the 95 chemically synthesized peptides were all specifically recognized by human immune sera, though at various prevalence. Peptide specific antibodies were obtained both by affinity-purification from malaria immune sera and by immunization of mice. These antibodies did not show significant cross reactions, i.e., they were specific for the original peptide, reacted with native parasite proteins in infected erythrocytes and several were active in inhibiting in vitro parasite growth. Circular dichroism studies indicated that the selected peptides assumed partial or high alpha-helical content. Thus, we demonstrate that the bioinformatics/chemical synthesis approach described here can lead to the rapid identification of molecules which target biologically active antibodies, thus identifying suitable vaccine candidates. This strategy can be, in principle, extended to vaccine discovery in a wide range of other pathogens.
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Affiliation(s)
- Viviane Villard
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - George W. Agak
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Géraldine Frank
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - Catherine Servis
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Issa Nébié
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Sodiomon B. Sirima
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | | | | | - Frederic Heitz
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Volker Bäcker
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | | | | | - Giampietro Corradin
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- * To whom correspondence should be addressed. E-mail:
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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.
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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
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Hong J, Kharenko OA, Ogawa MY. Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up. Inorg Chem 2007; 45:9974-84. [PMID: 17140193 PMCID: PMC2566827 DOI: 10.1021/ic060222j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.
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Shen W, Kornfield JA, Tirrell DA. Structure and mechanical properties of artificial protein hydrogels assembled through aggregation of leucine zipper peptide domains. SOFT MATTER 2006; 3:99-107. [PMID: 32680200 DOI: 10.1039/b610986a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Artificial protein hydrogels made from a triblock protein (designated AC10A, where A is an acidic zipper domain and C10 comprises 10 repeats of the nonapeptide sequence exhibit normalized plateau storage moduli (G'∞/nkT) less than 0.13 at all concentrations, pH values, and ionic strengths examined. These gels are surprisingly soft due to loop formation at the expense of bridges between physical junctions. Molecular-level evidence of loop formation is provided by strong fluorescence energy transfer (FRET) between distinct chromophores placed at the C- and N-termini of labelled chains diluted in an excess of unlabelled chains. The tendency to form loops originates from the compact size of the random coil midblock (mean RH(C10)≈ 20 Å, determined from quasi-elastic light scattering of C10), and is facilitated by the ability of the leucine zipper domains to form antiparallel aggregates. Although the aggregation number of the leucine zipper domains is small (tetrameric, determined from multi-angle static light scattering of AC10 diblock), the average center-to-center distance between aggregates is roughly 1.5 times the average end-to-end distance of the C10 domain in a 7% w/v network. To avoid stretching the C10 domain, the chains tend to form loops. Changes in pH or ionic strength that expand the polyelectrolyte midblock favor bridging, leading to greater G'∞ as long as leucine zipper endblocks do not dissociate. Understanding of the network structure provided successful design strategies to increase the rigidity of these hydrogels. In contrast to intuitive design concepts for rubber and gel materials, it was shown that increasing either the length or the charge density of the midblock increases rigidity, because fewer chains are wasted in loop formation.
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Affiliation(s)
- Wei Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
| | - Julia A Kornfield
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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44
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Liu J, Zheng Q, Deng Y, Kallenbach NR, Lu M. Conformational Transition between Four and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction. J Mol Biol 2006; 361:168-79. [PMID: 16828114 DOI: 10.1016/j.jmb.2006.05.063] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/19/2006] [Accepted: 05/24/2006] [Indexed: 11/21/2022]
Abstract
Alpha-helical coiled coils play a crucial role in mediating specific protein-protein interactions. However, the rules and mechanisms that govern helix-helix association in coiled coils remain incompletely understood. Here we have engineered a seven heptad "Phe-zipper" protein (Phe-14) with phenylalanine residues at all 14 hydrophobic a and d positions, and generated a further variant (Phe-14(M)) in which a single core Phe residue is substituted with Met. Phe-14 forms a discrete alpha-helical pentamer in aqueous solution, while Phe-14(M) folds into a tetrameric helical structure. X-ray crystal structures reveal that in both the tetramer and the pentamer the a and d side-chains interlock in a classical knobs-into-holes packing to produce parallel coiled-coil structures enclosing large tubular cavities. However, the presence of the Met residue in the apolar interface of the tetramer markedly alters its local coiled-coil conformation and superhelical geometry. Thus, short-range interactions involving the Met side-chain serve to preferentially select for tetramer formation, either by inhibiting a nucleation step essential for pentamer folding or by abrogating an intermediate required to form the pentamer. Although specific trigger sequences have not been clearly identified in dimeric coiled coils, higher-order coiled coils, as well as other oligomeric multi-protein complexes, may require such sequences to nucleate and direct their assembly.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA
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45
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Abstract
In this communication, we discuss the design, synthesis, and characterization of four peptides which are able to self-assemble into five different homo- and heterodimeric alpha-helical coiled coils based on the pH of their environment. These peptides are very short, containing only 14 or 21 amino acids each, and illustrate the minimum requirements necessary to form dimeric coiled coils which are critical in a large number of biological and materials design applications.
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Affiliation(s)
- He Dong
- Department of Chemistry and Bioengineering, Rice University, 6100 Main Street, Mail Stop 60, Houston, Texas 77005, USA
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46
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Yang J, Xu C, Wang C, Kopeèek J. Refolding hydrogels self-assembled from N-(2-hydroxypropyl)methacrylamide graft copolymers by antiparallel coiled-coil formation. Biomacromolecules 2006; 7:1187-95. [PMID: 16602737 PMCID: PMC2529150 DOI: 10.1021/bm051002k] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel hybrid hydrogel system based on N-(2-hydroxypropyl)methacrylamide copolymers was proposed. It consisted of the hydrophilic polymer backbone and a pair of oppositely charged peptide grafts. Two distinct pentaheptad peptides (CCE and CCK) were anticipated to create a dimerization motif and serve as physical cross-linkers. Consequently, the graft copolymers CCE-P and CCK-P self-assembled into hybrid hydrogels in situ; the process was modulated by the formation of antiparallel heterodimeric coiled-coils. This approach possesses an advantage to decrease the steric hindrance of the polymer backbone on the "in-register" alignment of peptide grafts. Indeed, equimolar mixtures of the graft copolymers, CCE-P/CCK-P, have been observed to self-assemble into hydrogels in PBS solution at neutral pH at concentrations as low as 0.1 wt %. Circular dichroism spectroscopy, sedimentation equilibrium experiments, and microrheology revealed that the self-assembly process corresponded to the two-stranded alpha-helical coiled-coil formation between CCE and CCK. Moreover, the formation of hybrid hydrogels was reversible. Denaturation of the coiled-coil domains with guanidine hydrochloride (GdnHCl) solutions resulted in disassembly of the hydrogels. Removal of GdnHCl by dialysis caused coiled-coil refolding and hydrogel reassembly. Scanning electron microscopy results demonstrated that the concentration of the graft copolymers had a significant impact on the structure and morphology of self-assembled hydrogels.
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Affiliation(s)
- Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Chunyu Xu
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Chun Wang
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jindøich Kopeèek
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, USA
- To whom correspondence should be addressed. E-mail:
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47
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48
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Matzapetakis M, Pecoraro VL. Site-selective metal binding by designed alpha-helical peptides. J Am Chem Soc 2006; 127:18229-33. [PMID: 16366576 DOI: 10.1021/ja055433m] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is known that the designed alpha-helical peptide family TRI [(Ac-G(LKALEEK)4G-CONH2)], containing single site substitution of a cysteine for a leucine, is capable of binding Cd(II) within a three-stranded coiled coil. The binding affinity of cadmium is dependent upon the site of substitution, with cysteine incorporated at the a site leading to cadmium complexes of higher affinity than when a d site was modified. In this work we have examined whether this differential binding affinity can be expressed in a di-cysteine-substituted peptide in order to develop site specificity within a designed system. The peptide TRI L9CL19C was used to determine whether significant differences in binding affinities at nearly proximal sites could be achieved in a short designed peptide. On the basis of 113Cd, 1H NMR, and circular dichroic spectroscopies, we have shown that 1 equiv of Cd(II) binds exclusively at the a site. Only after that position is filled does the second site become populated. Thus, the TRI system represents the first example where stoichiometrically equivalent peptides with different sequences form the framework for designing molecular assemblies that show site-specific ion recognition. We propose that the distinct metal affinities are due to the cysteine conformers at different substitution points along the peptide. Furthermore, we have shown that site selectivity in biomolecules can be encoded into relatively short peptides with helical sequences and, therefore, do not necessarily require the extensive protein scaffolds found in natural systems.
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Affiliation(s)
- Manolis Matzapetakis
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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49
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Shen W, Zhang K, Kornfield JA, Tirrell DA. Tuning the erosion rate of artificial protein hydrogels through control of network topology. NATURE MATERIALS 2006; 5:153-8. [PMID: 16444261 DOI: 10.1038/nmat1573] [Citation(s) in RCA: 208] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 12/06/2005] [Indexed: 05/06/2023]
Abstract
Erosion behaviour governs the use of physical hydrogels in biomedical applications ranging from controlled release to cell encapsulation. Genetically engineered protein hydrogels offer unique means of controlling the erosion rate by engineering their amino acid sequences and network topology. Here, we show that the erosion rate of such materials can be tuned by harnessing selective molecular recognition, discrete aggregation number and orientational discrimination of coiled-coil protein domains. Hydrogels formed from a triblock artificial protein bearing dissimilar helical coiled-coil end domains (P and A) erode more than one hundredfold slower than hydrogels formed from those bearing the same end domains (either P or A). The reduced erosion rate is a consequence of the fact that looped chains are suppressed because P and A tend not to associate with each other. Thus, the erosion rate can be tuned over several orders of magnitude in artificial protein hydrogels, opening the door to diverse biomedical applications.
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Affiliation(s)
- Wei Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA.
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50
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Farmer RS, Argust LM, Sharp JD, Kiick KL. Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups. Macromolecules 2006; 39:162-170. [PMID: 19180254 PMCID: PMC2632593 DOI: 10.1021/ma051534t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein engineering strategies have proven valuable for the production of a variety of well-defined macromolecular materials with controlled properties that have enabled their use in a range of materials and biological applications. In this work, such biosynthetic strategies have been employed in the production of monodisperse alanine-rich, helical protein polymers with the sequences [AAAQEAAAAQAAAQAEAAQAAQ](3) and [AAAQAAQAQAAAEAAAQAAQAQ](6). The composition of these protein polymers is similar to that of a previously reported family of alanine-rich protein polymers, but the density and placement of chemically reactive residues has been varied to facilitate the future use of these macromolecules in elucidating polymeric structure-function relationships in biological recognition events. Both protein polymers are readily expressed from E. coli and purified to homogeneity; characterization of their conformational behavior via circular dichroic spectroscopy (CD) indicates that they adopt highly helical conformations under a range of solution conditions. Differential scanning calorimetry, in concert with CD, demonstrates that the conformational transition from helix to coil in these macromolecules can be well-defined, with helicity, conformational transitions, T(m) values, and calorimetric enthalpies that vary with the molecular weight of the protein polymers. A combination of infrared spectroscopy and CD also reveals that the macromolecules can adopt beta-sheet structures at elevated temperatures and concentrations and that the existence and kinetics of this conformational transition appear to be related to the density of charged groups on the protein polymer.
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Affiliation(s)
- Robin S. Farmer
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Lindsey M. Argust
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Jared D. Sharp
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
| | - Kristi L. Kiick
- Department of Materials Science and Engineering and Delaware Biotechnology Institute, University of Delaware, 201 Dupont Hall, Newark, Delaware 19716
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