1
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Cole CC, Walker DR, Hulgan SAH, Pogostin BH, Swain JWR, Miller MD, Xu W, Duella R, Misiura M, Wang X, Kolomeisky AB, Philips GN, Hartgerink JD. Heterotrimeric collagen helix with high specificity of assembly results in a rapid rate of folding. Nat Chem 2024; 16:1698-1704. [PMID: 39009792 DOI: 10.1038/s41557-024-01573-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 06/06/2024] [Indexed: 07/17/2024]
Abstract
The most abundant natural collagens form heterotrimeric triple helices. Synthetic mimics of collagen heterotrimers have been found to fold slowly, even compared to the already slow rates of homotrimeric helices. These prolonged folding rates are not understood. Here we compare the stabilities, specificities and folding rates of three heterotrimeric collagen mimics designed through a computationally assisted approach. The crystal structure of one ABC-type heterotrimer verified a well-controlled composition and register and elucidated the geometry of pairwise cation-π and axial and lateral salt bridges in the assembly. This collagen heterotrimer folds much faster (hours versus days) than comparable, well-designed systems. Circular dichroism and NMR data suggest the folding is frustrated by unproductive, competing heterotrimer species and these species must unwind before refolding into the thermodynamically favoured assembly. The heterotrimeric collagen folding rate is inhibited by the introduction of preformed competing triple-helical assemblies, which suggests that slow heterotrimer folding kinetics are dominated by the frustration of the energy landscape caused by competing triple helices.
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Affiliation(s)
- Carson C Cole
- Department of Chemistry, Rice University, Houston, TX, USA
| | | | | | | | | | | | - Weijun Xu
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Ryan Duella
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Mikita Misiura
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Xu Wang
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
| | - George N Philips
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Jeffrey D Hartgerink
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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2
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Cole CC, Yu LT, Misiura M, Williams J, Bui TH, Hartgerink JD. Stabilization of Synthetic Collagen Triple Helices: Charge Pairs and Covalent Capture. Biomacromolecules 2023; 24:5083-5090. [PMID: 37871141 DOI: 10.1021/acs.biomac.3c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Collagen mimetic peptides are composed of triple helices. Triple helical formation frequently utilizes charge pair interactions to direct protein assembly. The design of synthetic triple helices is challenging due to the large number of competing species and the overall fragile nature of collagen mimetics. A successfully designed triple helix incorporates both positive and negative criteria to achieve maximum specificity of the supramolecular assembly. Intrahelical charge pair interactions, particularly those involved in lysine-aspartate and lysine-glutamate pairs, have been especially successful both in driving helix specificity and for subsequent stabilization by covalent capture. Despite this progress, the important sequential and geometric relationships of charged residues in a triple helical context have not been fully explored for either supramolecular assembly or covalent capture stabilization. In this study, we compare the eight canonical axial and lateral charge pairs of lysine and arginine with glutamate and aspartate to their noncanonical, reversed charge pairs. These findings are put into the context of collagen triple helical design and synthesis.
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Affiliation(s)
- Carson C Cole
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Le Tracy Yu
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Mikita Misiura
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Joseph Williams
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Thi H Bui
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jeffrey D Hartgerink
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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3
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Huang Y, Lan J, Wu C, Zhang R, Zheng H, Fan S, Xu F. Stability of collagen heterotrimer with same charge pattern and different charged residue identities. Biophys J 2023; 122:2686-2695. [PMID: 37226442 PMCID: PMC10397569 DOI: 10.1016/j.bpj.2023.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
Salt bridges are important factors in maintaining the stability of proteins, and their contribution to protein folding has received much attention. Although the interaction energies, or stabilizing contributions, of individual salt bridges have been measured in various proteins, a systematic assessment of various types of salt bridges in a relatively uniform environment is still a valuable analysis. Here, we used a collagen heterotrimer as a host-guest platform to construct 48 heterotrimers with the same charge pattern. A variety of salt bridges were formed between the oppositely charged residues Lys, Arg, Asp, and Glu. The melting temperature (Tm) of the heterotrimers was measured with circular dichroism. The atomic structures of 10 salt bridges were shown in three x-ray crystals of heterotrimer. Molecular dynamics simulation based on the crystal structures indicated that strong, intermediate, and weak salt bridges have distinctive N-O distances. A linear regression model was used to predict the stability of heterotrimers with high accuracy (R2 = 0.93). We developed an online database to help readers understand how a salt bridge stabilizes collagen. This work will help us better understand the stabilizing mechanism of salt bridges in collagen folding and provide a new strategy to design collagen heterotrimers.
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Affiliation(s)
- Yujie Huang
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jun Lan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Wu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ruixue Zhang
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hongning Zheng
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Shilong Fan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Fei Xu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China.
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4
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Ashrafichoobdar E, Perez T, Ayalew L, Gorbanwand V, Monroy J, Slowinska K. Hybrid peptides as platform for synchronized combination therapy. Colloids Surf B Biointerfaces 2023; 226:113326. [PMID: 37116378 DOI: 10.1016/j.colsurfb.2023.113326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
Combination therapy, where two or more therapeutic agents are combined to target different cellular pathways, is an effective tool in cancer treatment but often difficult to execute. Here we present the collagen peptide-based platform that allows for synchronous and colocalized cellular delivery of three different agents. The peptide is a hybrid between collagen and cell penetrating peptide (CPP) that assembles into a heterotrimer helix and forms fully organic, high aspect ratio nanoparticles. The validity of the approach was tested with three chemically different agents (Paclitaxel, Doxorubicin, and 5-Fluorouracil; a combination used in clinical treatment of (ER)-positive and (PR)-positive breast cancer) conjugated to N-terminus of the peptide. The design of this peptide-based drug delivery system provides several advantages: it avoids drug loading problems; removes the need for orthogonal synthesis; and allows for colocalized delivery of up to three drugs (which leads to the same biodistribution for each drug). In addition, hybrid collagen/CPP peptides are known to enhance cellular uptake and improve solubility of drugs. The synergistic effect, in terms of enhanced efficacy, of the Paclitaxel-Doxorubicin-5-Fluorouracil combination was also calculated. We envision self-assembling peptides as a platform for drug codelivery that can be expanded into a library of personalized combinations that may also include other functionalities like targeting or imaging.
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Affiliation(s)
- Elahe Ashrafichoobdar
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States
| | - Tanner Perez
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States
| | - Luladey Ayalew
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States
| | - Venus Gorbanwand
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States
| | - Joel Monroy
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States
| | - Katarzyna Slowinska
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, United States.
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5
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Bermeo S, Favor A, Chang YT, Norris A, Boyken SE, Hsia Y, Haddox HK, Xu C, Brunette TJ, Wysocki VH, Bhabha G, Ekiert DC, Baker D. De novo design of obligate ABC-type heterotrimeric proteins. Nat Struct Mol Biol 2022; 29:1266-1276. [PMID: 36522429 PMCID: PMC9758053 DOI: 10.1038/s41594-022-00879-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/20/2022] [Indexed: 12/23/2022]
Abstract
The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.
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Affiliation(s)
- Sherry Bermeo
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Andrew Favor
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Ya-Ting Chang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Andrew Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hugh K Haddox
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Chunfu Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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6
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Cole CC, Misiura M, Hulgan SAH, Peterson CM, Williams JW, Kolomeisky AB, Hartgerink JD. Cation-π Interactions and Their Role in Assembling Collagen Triple Helices. Biomacromolecules 2022; 23:4645-4654. [PMID: 36239387 DOI: 10.1021/acs.biomac.2c00856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cation-π interactions play a significant role in the stabilization of globular proteins. However, their role in collagen triple helices is less well understood and they have rarely been used in de novo designed collagen mimetic systems. In this study, we analyze the stabilizing and destabilizing effects in pairwise amino acid interactions between cationic and aromatic residues in both axial and lateral sequential relationships. Thermal unfolding experiments demonstrated that only axial pairs are stabilizing, while the lateral pairs are uniformly destabilizing. Molecular dynamics simulations show that pairs with an axial relationship can achieve a near-ideal interaction distance, but pairs in a lateral relationship do not. Arginine-π systems were found to be more stabilizing than lysine-π and histidine-π. Arginine-π interactions were then studied in more chemically diverse ABC-type heterotrimeric helices, where arginine-tyrosine pairs were found to form the best helix. This work helps elucidate the role of cation-π interactions in triple helices and illustrates their utility in designing collagen mimetic peptides.
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Affiliation(s)
- Carson C Cole
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Mikita Misiura
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Sarah A H Hulgan
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Caroline M Peterson
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Joseph W Williams
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D Hartgerink
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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7
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Malcor JD, Mallein-Gerin F. Biomaterial functionalization with triple-helical peptides for tissue engineering. Acta Biomater 2022; 148:1-21. [PMID: 35675889 DOI: 10.1016/j.actbio.2022.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022]
Abstract
In the growing field of tissue engineering, providing cells in biomaterials with the adequate biological cues represents an increasingly important challenge. Yet, biomaterials with excellent mechanical properties often are often biologically inert to many cell types. To address this issue, researchers resort to functionalization, i.e. the surface modification of a biomaterial with active molecules or substances. Functionalization notably aims to replicate the native cellular microenvironment provided by the extracellular matrix, and in particular by collagen, its major component. As our understanding of biological processes regulating cell behaviour increases, functionalization with biomolecules binding cell surface receptors constitutes a promising strategy. Amongst these, triple-helical peptides (THPs) that reproduce the architectural and biological properties of collagen are especially attractive. Indeed, THPs containing binding sites from the native collagen sequence have successfully been used to guide cell response by establishing cell-biomaterial interactions. Notably, the GFOGER motif recognising the collagen-binding integrins is extensively employed as a cell adhesive peptide. In biomaterials, THPs efficiently improved cell adhesion, differentiation and function on biomaterials designed for tissue repair (especially for bone, cartilage, tendon and heart), vascular graft fabrication, wound dressing, drug delivery or immunomodulation. This review describes the key characteristics of THPs, their effect on cells when combined to biomaterials and their strong potential as biomimetic tools for regenerative medicine. STATEMENT OF SIGNIFICANCE: This review article describes how triple-helical peptides constitute efficient tools to improve cell-biomaterial interactions in tissue engineering. Triple helical peptides are bioactive molecules that mimic the architectural and biological properties of collagen. They have been successfully used to specifically recognize cell-surface receptors and provide cells seeded on biomaterials with controlled biological cues. Functionalization with triple-helical peptides has enabled researchers to improve cell function for regenerative medicine applications, such as tissue repair. However, despite encouraging results, this approach remains limited and under-exploited, and most functionalization strategies reported in the literature rely on biomolecules that are unable to address collagen-binding receptors. This review will assist researchers in selecting the correct tools to functionalize biomaterials in efforts to guide cellular response.
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Affiliation(s)
- Jean-Daniel Malcor
- Laboratory of Tissue Biology and Therapeutic Engineering, CNRS UMR 5305, University Claude Bernard-Lyon 1 and University of Lyon, 7 Passage du Vercors, Cedex 07, Lyon 69367, France.
| | - Frédéric Mallein-Gerin
- Laboratory of Tissue Biology and Therapeutic Engineering, CNRS UMR 5305, University Claude Bernard-Lyon 1 and University of Lyon, 7 Passage du Vercors, Cedex 07, Lyon 69367, France
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8
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Xu Y, Kirchner M. Collagen Mimetic Peptides. Bioengineering (Basel) 2021; 8:5. [PMID: 33466358 PMCID: PMC7824840 DOI: 10.3390/bioengineering8010005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022] Open
Abstract
Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix-the building block of collagen-and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs-their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies.
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Affiliation(s)
- Yujia Xu
- Department of Chemistry, Hunter College of the City University of New York, 695 Park Ave., New York, NY 10065, USA;
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9
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Hulgan SAH, Jalan AA, Li IC, Walker DR, Miller MD, Kosgei AJ, Xu W, Phillips GN, Hartgerink JD. Covalent Capture of Collagen Triple Helices Using Lysine–Aspartate and Lysine–Glutamate Pairs. Biomacromolecules 2020; 21:3772-3781. [DOI: 10.1021/acs.biomac.0c00878] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sarah A. H. Hulgan
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Abhishek A. Jalan
- Department of Biochemistry, University of Bayreuth, Bayreuth 95447, Germany
| | - I-Che Li
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Douglas R. Walker
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Mitchell D. Miller
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Abigael J. Kosgei
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Weijun Xu
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - George N. Phillips
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D. Hartgerink
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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10
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Li IC, Hulgan SAH, Walker DR, Farndale RW, Hartgerink JD, Jalan AA. Covalent Capture of a Heterotrimeric Collagen Helix. Org Lett 2019; 21:5480-5484. [DOI: 10.1021/acs.orglett.9b01771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- I-Che Li
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Sarah A. H. Hulgan
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Douglas R. Walker
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Richard W. Farndale
- University of Cambridge Department of Biochemistry, Downing Site, Cambridge CB2 1QW, U.K
| | - Jeffrey D. Hartgerink
- Rice University Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Abhishek A. Jalan
- University of Bayreuth Department of Biochemistry, Universitätsstraße 30, Bayreuth 95447, Germany
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11
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12
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A cysteine-based molecular code informs collagen C-propeptide assembly. Nat Commun 2018; 9:4206. [PMID: 30310058 PMCID: PMC6181919 DOI: 10.1038/s41467-018-06185-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 08/23/2018] [Indexed: 11/29/2022] Open
Abstract
Fundamental questions regarding collagen biosynthesis, especially with respect to the molecular origins of homotrimeric versus heterotrimeric assembly, remain unanswered. Here, we demonstrate that the presence or absence of a single cysteine in type-I collagen’s C-propeptide domain is a key factor governing the ability of a given collagen polypeptide to stably homotrimerize. We also identify a critical role for Ca2+ in non-covalent collagen C-propeptide trimerization, thereby priming the protein for disulfide-mediated covalent immortalization. The resulting cysteine-based code for stable assembly provides a molecular model that can be used to predict, a priori, the identity of not just collagen homotrimers, but also naturally occurring 2:1 and 1:1:1 heterotrimers. Moreover, the code applies across all of the sequence-diverse fibrillar collagens. These results provide new insight into how evolution leverages disulfide networks to fine-tune protein assembly, and will inform the ongoing development of designer proteins that assemble into specific oligomeric forms. Collagen proteins assemble into trimers from distinct monomers with high specificity, yet the molecular basis for this specificity remains unclear. Here the authors demonstrate the crucial role of conserved C-terminal domain cysteine residues and calcium in homotrimeric procollagen assembly.
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13
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Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest. Biochem J 2018; 475:3123-3140. [PMID: 30315001 DOI: 10.1042/bcj20180482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022]
Abstract
The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.
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14
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How electrostatic networks modulate specificity and stability of collagen. Proc Natl Acad Sci U S A 2018; 115:6207-6212. [PMID: 29844169 DOI: 10.1073/pnas.1802171115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.
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15
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Abstract
Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.
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Affiliation(s)
- Danielle M Raymond
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA.
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16
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Yin Z, Wu F, Zheng Z, Kaplan DL, Kundu SC, Lu S. Self-Assembling Silk-Based Nanofibers with Hierarchical Structures. ACS Biomater Sci Eng 2017; 3:2617-2627. [DOI: 10.1021/acsbiomaterials.7b00442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zhuping Yin
- National
Engineering Laboratory for Modern Silk, College of Textile and Clothing
Engineering, Soochow University, Suzhou 215123, China
| | - Feng Wu
- National
Engineering Laboratory for Modern Silk, College of Textile and Clothing
Engineering, Soochow University, Suzhou 215123, China
| | - Zhaozhu Zheng
- National
Engineering Laboratory for Modern Silk, College of Textile and Clothing
Engineering, Soochow University, Suzhou 215123, China
| | - David L. Kaplan
- National
Engineering Laboratory for Modern Silk, College of Textile and Clothing
Engineering, Soochow University, Suzhou 215123, China
- Department
of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Subhas C. Kundu
- 3Bs
Research Group, Headquarters of the European Institute of Excellence
on Tissue Engineering and Regenerative Medicine, University of Minho, AvePark, 4805-017 Barco, Guimarãdes, Portugal
| | - Shenzhou Lu
- National
Engineering Laboratory for Modern Silk, College of Textile and Clothing
Engineering, Soochow University, Suzhou 215123, China
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17
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Zhao F, Guo H, Zhang Z, Ye J, Liu L, Zhao CX, Shao Z. Conformation and self-assembly changes of isomeric peptide amphiphiles influenced by switching tyrosine in the sequences. J Mater Chem B 2017; 5:5189-5195. [DOI: 10.1039/c7tb00736a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
By simply switching the location of Tyr in isomeric peptide amphiphiles of C12-(GA)3GY, the varied conformations between the β-sheet and disordered one of these peptide amphiphiles and the alternating morphologies between nanofibers and nanospheres of their assemblies are revealed.
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Affiliation(s)
- Fangyi Zhao
- State Key Laboratory of Molecular Engineering of Polymers
- Laboratory of Advanced Materials and Department of Macromolecular Science
- Fudan University
- Shanghai 200433
- China
| | - Hui Guo
- State Key Laboratory of Molecular Engineering of Polymers
- Laboratory of Advanced Materials and Department of Macromolecular Science
- Fudan University
- Shanghai 200433
- China
| | - Zhidong Zhang
- State Key Laboratory of Molecular Engineering of Polymers
- Laboratory of Advanced Materials and Department of Macromolecular Science
- Fudan University
- Shanghai 200433
- China
| | - John Ye
- Peptide Scientific Inc
- Fairfiled NJ 07004
- USA
| | | | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology
- The University of Queensland
- St. Lucia
- Australia
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers
- Laboratory of Advanced Materials and Department of Macromolecular Science
- Fudan University
- Shanghai 200433
- China
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18
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Kumar VA, Wang BK, Kanahara SM. Rational design of fiber forming supramolecular structures. Exp Biol Med (Maywood) 2016; 241:899-908. [PMID: 27022140 PMCID: PMC4950345 DOI: 10.1177/1535370216640941] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/24/2016] [Indexed: 12/28/2022] Open
Abstract
Recent strides in the development of multifunctional synthetic biomimetic materials through the self-assembly of multi-domain peptides and proteins over the past decade have been realized. Such engineered systems have wide-ranging application in bioengineering and medicine. This review focuses on fundamental fiber forming α-helical coiled-coil peptides, peptide amphiphiles, and amyloid-based self-assembling peptides; followed by higher order collagen- and elastin-mimetic peptides with an emphasis on chemical / biological characterization and biomimicry.
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Affiliation(s)
| | | | - Satoko M Kanahara
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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19
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Sun X, Fan J, Li X, Zhang S, Liu X, Xiao J. Colorimetric and fluorometric monitoring of the helix composition of collagen-like peptides at the nM level. Chem Commun (Camb) 2016; 52:3107-10. [PMID: 26692232 DOI: 10.1039/c5cc09565d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have demonstrated that the incorporation of a dye-labeled collagen-like peptide in the homotrimeric versus heterotrimeric context results in visible color changes and distinct fluorescence. The unique fluorescence self-quenching assay can unambiguously determine the helix composition of heterotrimers at the nM level, far extending our capability to characterize a collagen triple helix.
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Affiliation(s)
- Xiuxia Sun
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Jun Fan
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Xuan Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Shanshan Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Xiaoyan Liu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Jianxi Xiao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
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20
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Acevedo-Jake AM, Clements KA, Hartgerink JD. Synthetic, Register-Specific, AAB Heterotrimers to Investigate Single Point Glycine Mutations in Osteogenesis Imperfecta. Biomacromolecules 2016; 17:914-21. [DOI: 10.1021/acs.biomac.5b01562] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Amanda M. Acevedo-Jake
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street. Houston, Texas 77005, United States
| | - Katherine A. Clements
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street. Houston, Texas 77005, United States
| | - Jeffrey D. Hartgerink
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street. Houston, Texas 77005, United States
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21
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Sun X, Fan J, Ye W, Zhang H, Cong Y, Xiao J. A highly specific graphene platform for sensing collagen triple helix. J Mater Chem B 2016; 4:1064-1069. [DOI: 10.1039/c5tb02218e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have designed a dye-labeled, highly positively charged single stranded collagen (ssCOL) peptide probe whose adsorption into GO quenches its fluorescence. The hybridization of the ssCOL probe with a complementary target sequence forms a triple stranded collagen (tsCOL) peptide, resulting in the retention of the fluorescence of the probe.
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Affiliation(s)
- Xiuxia Sun
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Jun Fan
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Weiran Ye
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Han Zhang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Yong Cong
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
| | - Jianxi Xiao
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
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22
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Sun X, Liu S, Yu W, Wang S, Xiao J. CD and NMR investigation of collagen peptides mimicking a pathological Gly-Ser mutation and a natural interruption in a similar highly charged sequence context. Protein Sci 2015; 25:383-92. [PMID: 26457583 DOI: 10.1002/pro.2828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 12/29/2022]
Abstract
Even a single Gly substitution in the triple helix domain of collagen leads to pathological conditions while natural interruptions are suggested to play important functional roles. Two peptides-one mimicking a pathological Gly-Ser substitution (ERSEQ) and the other one modeling a similar natural interruption sequence (DRSER)-are designed to facilitate the comparison for elucidating the molecular basis of their different biological roles. CD and NMR investigation of peptide ERSEQ indicates a reduction of the thermal stability and disruption of hydrogen bonding at the Ser mutation site, providing a structural basis of the OI disease resulting from the Gly-Ser mutation in the highly charged RGE environment. Both CD and NMR real-time folding results indicate that peptide ERSEQ displays a comparatively slower folding rate than peptide DRSER, suggesting that the Gly-Ser mutation may lead to a larger interference in folding than the natural interruption in a similar RSE context. Our studies suggest that unlike the rigid GPO environment, the abundant R(K)GE(D) motif may provide a more flexible sequence environment that better accommodates mutations as well as interruptions, while the electrostatic interactions contribute to its stability. These results shed insight into the molecular features of the highly charged motif and may aid the design of collagen biomimetic peptides containing important biological sites.
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Affiliation(s)
- Xiuxia Sun
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Songqing Liu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Wenyuan Yu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Jianxi Xiao
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
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23
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Xiao J, Sun X, Madhan B, Brodsky B, Baum J. NMR studies demonstrate a unique AAB composition and chain register for a heterotrimeric type IV collagen model peptide containing a natural interruption site. J Biol Chem 2015. [PMID: 26209635 DOI: 10.1074/jbc.m115.654871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
All non-fibrillar collagens contain interruptions in the (Gly-X-Y)n repeating sequence, such as the more than 20 interruptions found in chains of basement membrane type IV collagen. Two selectively doubly labeled peptides are designed to model a site in type IV collagen with a GVG interruption in the α1(IV) and a corresponding GISLK sequence within the α2(IV) chain. CD and NMR studies on a 2:1 mixture of these two peptides support the formation of a single-component heterotrimer that maintains the one-residue staggering in the triple-helix, has a unique chain register, and contains hydrogen bonds at the interruption site. Formation of hydrogen bonds at interruption sites may provide a driving force for self-assembly and chain register in type IV and other non-fibrillar collagens. This study illustrates the potential role of interruptions in the structure, dynamics, and folding of natural collagen heterotrimers and forms a basis for understanding their biological role.
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Affiliation(s)
- Jianxi Xiao
- the Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China, From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Xiuxia Sun
- the Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Balaraman Madhan
- the Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600020, India
| | - Barbara Brodsky
- the Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02446, and
| | - Jean Baum
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854,
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24
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Jiang T, Vail OA, Jiang Z, Zuo X, Conticello VP. Rational Design of Multilayer Collagen Nanosheets with Compositional and Structural Control. J Am Chem Soc 2015; 137:7793-802. [DOI: 10.1021/jacs.5b03326] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Jiang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Owen A. Vail
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhigang Jiang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Xiaobing Zuo
- X-ray
Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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25
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Xiao J, Yang Z, Sun X, Addabbo R, Baum J. Local amino acid sequence patterns dominate the heterogeneous phenotype for the collagen connective tissue disease Osteogenesis Imperfecta resulting from Gly mutations. J Struct Biol 2015; 192:127-37. [PMID: 25980613 DOI: 10.1016/j.jsb.2015.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/08/2015] [Accepted: 05/10/2015] [Indexed: 12/30/2022]
Abstract
Osteogenesis Imperfecta (OI), a hereditary connective tissue disease in collagen that arises from a single Gly → X mutation in the collagen chain, varies widely in phenotype from perinatal lethal to mild. It is unclear why there is such a large variation in the severity of the disease considering the repeating (Gly-X-Y)n sequence and the uniform rod-like structure of collagen. We systematically evaluate the effect of local (Gly-X-Y)n sequence around the mutation site on OI phenotype using integrated bio-statistical approaches, including odds ratio analysis and decision tree modeling. We show that different Gly → X mutations have different local sequence patterns that are correlated with lethal and nonlethal phenotypes providing a mechanism for understanding the sensitivity of local context in defining lethal and non-lethal OI. A number of important trends about which factors are related to OI phenotypes are revealed by the bio-statistical analyses; most striking is the complementary relationship between the placement of Pro residues and small residues and their correlation to OI phenotype. When Pro is present or small flexible residues are absent nearby a mutation site, the OI case tends to be lethal; when Pro is present or small flexible residues are absent further away from the mutation site, the OI case tends to be nonlethal. The analysis also reveals the dominant role of local sequence around mutation sites in the Major Ligand Binding Regions that are primarily responsible for collagen binding to its receptors and shows that non-lethal mutations are highly predicted by local sequence considerations alone whereas lethal mutations are not as easily predicted and may be a result of more complex interactions. Understanding the sequence determinants of OI mutations will enhance genetic counseling and help establish which steps in the collagen hierarchy to target for drug therapy.
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Affiliation(s)
- Jianxi Xiao
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, United States; State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Zhangfu Yang
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiuxia Sun
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Rayna Addabbo
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, United States
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, United States.
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26
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Acevedo-Jake AM, Jalan AA, Hartgerink JD. Comparative NMR Analysis of Collagen Triple Helix Organization from N- to C-Termini. Biomacromolecules 2014; 16:145-55. [DOI: 10.1021/bm501281a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Amanda M. Acevedo-Jake
- Departments of Chemistry
and Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Abhishek A. Jalan
- Departments of Chemistry
and Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Jeffrey D. Hartgerink
- Departments of Chemistry
and Bioengineering, Rice University, Houston, Texas 77030, United States
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27
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Sarkar B, O'Leary LER, Hartgerink JD. Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation. J Am Chem Soc 2014; 136:14417-24. [PMID: 25494829 DOI: 10.1021/ja504377s] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mimicking the multistep self-assembly of the fibrillar protein collagen is an important design challenge in biomimetic supramolecular chemistry. Utilizing the complementarity of oppositely charged domains in short collagen-like peptides, we have devised a strategy for the self-assembly of these peptides into fibers. The strategy depends on the formation of a staggered triple helical species facilitated by interchain charged pairs, and is inspired by similar sticky-ended fibrillation designs applied in DNA and coiled coil fibers. We compare two classes of collagen mimetic peptides with the same composition but different domain arrangements, and show that differences in their proposed nucleation events differentiates their fibrillation capabilities. Larger nucleation domains result in rapid fiber formation and eventual precipitation or gelation while short nucleation domains leave the peptide soluble for long periods of time. For one of the fiber-forming peptides, we elucidate the packing parameters by X-ray diffraction.
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Affiliation(s)
- Biplab Sarkar
- Department of Chemistry and ‡Department of Bioengineering, Rice University , Houston, Texas 77005, United States
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28
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Jalan AA, Jochim KA, Hartgerink JD. Rational Design of a Non-canonical “Sticky-Ended” Collagen Triple Helix. J Am Chem Soc 2014; 136:7535-8. [DOI: 10.1021/ja5001246] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Abhishek A. Jalan
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Katherine A. Jochim
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D. Hartgerink
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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29
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Parmar AS, Joshi M, Nosker PL, Hasan NF, Nanda V. Control of Collagen Stability and Heterotrimer Specificity through Repulsive Electrostatic Interactions. Biomolecules 2013; 3:986-96. [PMID: 24970200 PMCID: PMC4030969 DOI: 10.3390/biom3040986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 11/16/2022] Open
Abstract
Charge-pair interactions between acidic and basic residues on the surface of collagen can promote stability as well as control specificity of molecular recognition. Heterotrimeric collagen peptides have been engineered de novo using either rational or computational methods, which in both cases optimize networks of favorable charge-pair interactions in the target structure. Less understood is the role of electrostatic repulsion between groups of like charge in destabilizing structure or directing molecular recognition. To study this, we apply a "charge crowding" approach, where repulsive interactions between multiple aspartate side chains are found to destabilize the homotrimer states in triple helical peptide system and can be utilized to promote the formation of heterotrimers. Neutralizing surface charge by increasing salt concentration or decreasing pH can enhance homotrimer stability, confirming the role of charge crowding on the destabilization of homotrimers via electrostatic repulsion. Charge crowding may be used in conjunction with other approaches to create specific collagen heterotrimers.
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Affiliation(s)
- Avanish S Parmar
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 679 Hoes Lane W, Piscataway, NJ 08854, USA.
| | - Mihir Joshi
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 679 Hoes Lane W, Piscataway, NJ 08854, USA.
| | - Patrick L Nosker
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 679 Hoes Lane W, Piscataway, NJ 08854, USA.
| | - Nida F Hasan
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 679 Hoes Lane W, Piscataway, NJ 08854, USA.
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, 679 Hoes Lane W, Piscataway, NJ 08854, USA.
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30
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Berisio R, Vitagliano L. Polyproline and triple helix motifs in host-pathogen recognition. Curr Protein Pept Sci 2013; 13:855-65. [PMID: 23305370 PMCID: PMC3707005 DOI: 10.2174/138920312804871157] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/10/2012] [Accepted: 08/30/2012] [Indexed: 01/18/2023]
Abstract
Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating host-pathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.
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Affiliation(s)
- Rita Berisio
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy
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31
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Guo H, Zhang J, Xu T, Zhang Z, Yao J, Shao Z. The Robust Hydrogel Hierarchically Assembled from a pH Sensitive Peptide Amphiphile Based on Silk Fibroin. Biomacromolecules 2013; 14:2733-8. [DOI: 10.1021/bm4005645] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hui Guo
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
| | - Jinming Zhang
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
| | - Tao Xu
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
| | - Zhidong Zhang
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
| | - Jinrong Yao
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
| | - Zhengzhong Shao
- State Key Laboratory of Molecule Engineering of Polymers,
Laboratory of Advanced Materials and Department of Macromolecular
Science, Fudan University, 220 Handan Road,
Shanghai 200433, People’s Republic of China
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32
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Jalan AA, Demeler B, Hartgerink JD. Hydroxyproline-free single composition ABC collagen heterotrimer. J Am Chem Soc 2013; 135:6014-7. [PMID: 23574286 PMCID: PMC3663077 DOI: 10.1021/ja402187t] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxyproline plays a major role in stabilizing collagenous domains in eukaryotic organisms. Lack of this modification is associated with significant lowering in the thermal stability of the collagen triple helix and may also affect fibrillogenesis and folding of the peptide chains. In contrast, even though bacterial collagens lack hydroxyproline, their thermal stability is comparable to that of fibrillar collagen. This has been attributed to the high frequency of charged amino acids found in bacterial collagen. Here we report a thermally stable hydroxyproline-free ABC heterotrimeric collagen mimetic system composed of decapositive and decanegative peptides and a zwitterionic peptide. None of the peptides contain hydroxyproline, and furthermore the zwitterionic peptide does not even contain proline. The heterotrimer is electrostatically stabilized via multiple interpeptide lysine-aspartate and lysine-glutamate salt bridges and maintains good thermal stability with a melting temperature of 37 °C. The ternary peptide mixture also populates a single composition ABC heterotrimer as confirmed by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. This system illustrates the power of axial salt bridges to direct and stabilize the self-assembly of a triple helix and may be useful in analogous designs in expression systems where the incorporation of hydroxyproline is challenging.
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Affiliation(s)
- Abhishek A. Jalan
- Department of Chemistry, Rice University, 6100 Main St., Houston, TX 77005
| | - Borries Demeler
- Department of Biochemistry, U. T Health Science Center, San Antonio, TX 78229
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Parmar AS, Zahid S, Belure SV, Young R, Hasan N, Nanda V. Design of net-charged abc-type collagen heterotrimers. J Struct Biol 2013; 185:163-7. [PMID: 23603270 DOI: 10.1016/j.jsb.2013.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/05/2013] [Accepted: 04/08/2013] [Indexed: 10/26/2022]
Abstract
Net-negatively-charged heterospecific A:B:C collagen peptide heterotrimers were designed using an automated computational approach. The design algorithm considers both target stability and the energy gap between the target states and misfolded competing states. Structural characterization indicates the net-negative charge balance on the new designs enhances the specificity of the target state at the expense of its stability.
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Affiliation(s)
- Avanish S Parmar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
| | - Sohail Zahid
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
| | - Sandeep V Belure
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
| | - Robert Young
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
| | - Nida Hasan
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ and Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, United States.
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Jalan AA, Hartgerink JD. Simultaneous control of composition and register of an AAB-type collagen heterotrimer. Biomacromolecules 2012; 14:179-85. [PMID: 23210738 DOI: 10.1021/bm3015818] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Control over composition and register of the peptide chains in AAB-type collagen mimetic heterotrimers is critical in developing systems that show fidelity to native collagen. However, their design is challenging due to the eight competing states possible for a mixture of nonidentical peptides A and B. Interpeptide salt-bridges have been used previously as keystone interactions to bias the population of competing states to favor a target heterotrimer. The designed heterotrimers were electroneutral and relied on pairing of acidic and basic residues but could not differentiate between all of the competing states and reported systems populated either multiple heterotrimer compositions or registers. Here our design methodology includes both positive and negative elements. First, an excess of acidic or basic residues, which always remain unpaired, introduces a negative design component to destabilize the competing triple helical compositions and registers. Second, charge pairs introduce a positive design component and stabilize the target assembly. These antagonistic factors are optimized in the target heterotrimer that forms the maximum number of charge pairs and minimizes unpaired charged residues. Additionally, we find that not just the number of paired and unpaired residues are important, but also the type. By a systematic study of different types of charge pairs and unpaired residues, we are able to populate a single composition-single register AAB heterotrimer. The insights gained here may be useful in designing composition and register specific heterotrimeric ligands with domains that recognize collagen-binding proteins.
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Affiliation(s)
- Abhishek A Jalan
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
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Giddu S, Xu F, Nanda V. Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer. Proteins 2012; 81:386-93. [PMID: 23042255 DOI: 10.1002/prot.24194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/12/2012] [Accepted: 10/02/2012] [Indexed: 11/11/2022]
Abstract
Stability of the collagen triple helix is largely governed by its imino acid content, namely the occurrence of proline and 4R-hydroxyproline at the X and Y positions, respectively, of the periodic (Gly-X-Y)(n) sequence. Although other amino acids at these positions reduce stability of the triple helix, this can be partially compensated by introducing intermolecular side-chain salt bridges. This approach was previously used to design an abc-type heterotrimer composed of one basic, one acidic, and one neutral imino acid rich chain (Gauba and Hartgerink, J Am Chem Soc 2007;129:15034-15041). In this study, an abc-type heterotrimer was designed to be the most stable species using a sequence recombination strategy that preserved both the amino acid composition and the network of interchain salt bridges of the original design. The target heterotrimer had the highest T(m) of 50 °C, 7 °C greater than the next most stable species. Stability of the heterotrimer decreased with increasing ionic strength, consistent with the role of intermolecular salt bridges in promoting stability. Quantitative meta-analysis of these results and published stability measurements on closely related peptides was used to discriminate the contributions of backbone propensity and side-chain electrostatics to collagen stability.
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Affiliation(s)
- Sumana Giddu
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
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Computational design of self-assembling register-specific collagen heterotrimers. Nat Commun 2012; 3:1087. [DOI: 10.1038/ncomms2084] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/22/2012] [Indexed: 01/13/2023] Open
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