1
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Fiala T, Bittner P, Heeb R, Islami V, Söll C, Pruška A, Zenobi R, Wennemers H. Hyperstable, Minimal-Length, and Blunt-Ended Collagen Heterotrimers. Angew Chem Int Ed Engl 2025:e202503353. [PMID: 40344344 DOI: 10.1002/anie.202503353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 05/07/2025] [Accepted: 05/08/2025] [Indexed: 05/11/2025]
Abstract
Most natural collagens are heterotrimers-triple helices formed from three non-identical peptide strands. The design of synthetic heterotrimeric collagen is challenging since a mixture of three different peptides can form as many as 27 unique triple helices. Here, we present a general method for the assembly of collagen heterotrimers with a wide range of lengths, thermal stabilities, and strand arrangements driven by complementary interstrand salt bridges between (2S,4S)-4-aminoproline and aspartate residues. We show how kinetic trapping of undesired trimers can be overcome by adjusting the annealing conditions to obtain the target heterotrimeric helix selectively under thermodynamic control. The design rules and annealing methods allowed the creation of the most stable supramolecular heterotrimer (32 residues, Tm = 76 °C) and the shortest stable heterotrimer (17 residues, Tm = 19 °C) to date. Furthermore, frame-shifting enabled, for the first time, the creation of a collagen triple helix with blunt ends.
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Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Philipp Bittner
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Rahel Heeb
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Valdrin Islami
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Carolina Söll
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Adam Pruška
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
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2
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Bächinger HP, Boudko SP. Mysteries of the collagen triple helix. Matrix Biol 2025; 137:12-18. [PMID: 39956287 DOI: 10.1016/j.matbio.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Revised: 02/07/2025] [Accepted: 02/10/2025] [Indexed: 02/18/2025]
Abstract
The collagen triple helix is one of the structurally simplest protein motifs that still holds a lot of secrets. The Gly-X-Y repeat is a business card of collagens, where Gly is required for the tight packing of three helices into a superhelix and X and Y residues are important for stabilizing the triple helix and communicating with the world. On its way to a functional molecule, collagen sequences undergo unique post-translational modifications inside and outside of the cell. Moreover, folding and secretion of collagens require specific proteins and mechanisms. Cracking the collagen triple helix codes opens up opportunities for curing associated diseases and developing new biomaterials. Here, we summarized my journey through some mysteries of the collagen triple helix and point out key unaddressed questions and problems for other researchers to pursue.
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Affiliation(s)
- Hans Peter Bächinger
- Research Department, Shriners Hospital for Children, Portland, OR, USA; Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, USA.
| | - Sergei P Boudko
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
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3
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Malcor JD, Ferruz N, Romero-Romero S, Dhingra S, Sagar V, Jalan AA. Deciphering the folding code of collagens. Nat Commun 2025; 16:2702. [PMID: 40108160 PMCID: PMC11923368 DOI: 10.1038/s41467-024-54046-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 10/30/2024] [Indexed: 03/22/2025] Open
Abstract
Collagen proteins contain a characteristic structural motif called a triple helix. During the self-assembly of this motif, three polypeptides form a folding nucleus at the C-termini and then propagate towards the N-termini like a zip-chain. While polypeptides from human collagens contain up to a 1000 amino acids, those found in bacteria can contain up to 6000 amino acids. Additionally, the collagen polypeptides are also frequently interrupted by non-helical sequences that disrupt folding and reduce stability. Given the length of polypeptides and the disruptive interruptions, compensating mechanisms that stabilize against local unfolding during propagation and offset the entropic cost of folding are not fully understood. Here, we show that the information for the correct folding of collagen triple helices is encoded in their sequence as interchain electrostatic interactions, which likely act as molecular clamps that prevent local unfolding. In the case of humans, disrupting these electrostatic interactions is associated with severe to lethal diseases.
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Affiliation(s)
- Jean-Daniel Malcor
- Laboratory of Tissue Biology and Therapeutic Engineering, CNRS UMR 5305 University of Lyon, Lyon, France
| | - Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Centre for Genomic Regulation, Barcelona, Spain
| | - Sergio Romero-Romero
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Department of Biochemistry and Structural Biology. Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Surbhi Dhingra
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Vamika Sagar
- Department of Biomaterials, University of Bayreuth, Bayreuth, Germany
| | - Abhishek A Jalan
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Department of Biomaterials, University of Bayreuth, Bayreuth, Germany.
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4
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Wang ZZ, Wang K, Xu LF, Su C, Gong JS, Shi JS, Ma XD, Xie N, Qian JY. Unlocking the Potential of Collagenases: Structures, Functions, and Emerging Therapeutic Horizons. BIODESIGN RESEARCH 2024; 6:0050. [PMID: 39381623 PMCID: PMC11458858 DOI: 10.34133/bdr.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/06/2024] [Accepted: 08/31/2024] [Indexed: 10/10/2024] Open
Abstract
Collagenases, a class of enzymes that are specifically responsible for collagen degradation, have garnered substantial attention because of their pivotal roles in tissue repair, remodeling, and medical interventions. This comprehensive review investigates the diversity, structures, and mechanisms of collagenases and highlights their therapeutic potential. First, it provides an overview of the biochemical properties of collagen and highlights its importance in extracellular matrix function. Subsequently, it meticulously analyzes the sources of collagenases and their applications in tissue engineering and food processing. Notably, this review emphasizes the predominant role played by microbial collagenases in commercial settings while discussing their production and screening methods. Furthermore, this study elucidates the methodology employed for determining collagenase activity and underscores the importance of an accurate evaluation for both research purposes and clinical applications. Finally, this review highlights the future research prospects for collagenases, with a particular focus on promoting wound healing and treating scar tissue formation and fibrotic diseases.
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Affiliation(s)
- Zhen-Zhen Wang
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Kang Wang
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Ling-Feng Xu
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Chang Su
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
| | - Xu-Dong Ma
- Cytori Therapeutics LLC., Shanghai 201802, PR China
| | - Nan Xie
- Cytori Therapeutics LLC., Shanghai 201802, PR China
| | - Jian-Ying Qian
- School of Life Sciences and Health Engineering,
Jiangnan University, Wuxi 214122, PR China
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5
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Saini RS, Binduhayyim RIH, Gurumurthy V, Alshadidi AAF, Bavabeedu SS, Vyas R, Dermawan D, Naseef PP, Mosaddad SA, Heboyan A. In silico assessment of biocompatibility and toxicity: molecular docking and dynamics simulation of PMMA-based dental materials for interim prosthetic restorations. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2024; 35:28. [PMID: 38833196 PMCID: PMC11150300 DOI: 10.1007/s10856-024-06799-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
AIM This study aimed to comprehensively assess the biocompatibility and toxicity profiles of poly(methyl methacrylate) (PMMA) and its monomeric unit, methyl methacrylate (MMA), crucial components in dental materials for interim prosthetic restorations. METHODOLOGY Molecular docking was employed to predict the binding affinities, energetics, and steric features of MMA and PMMA with selected receptors involved in bone metabolism and tissue development, including RANKL, Fibronectin, BMP9, NOTCH2, and other related receptors. The HADDOCK standalone version was utilized for docking calculations, employing a Lamarckian genetic algorithm to explore the conformational space of ligand-receptor interactions. Furthermore, molecular dynamics (MD) simulations over 100 nanoseconds were conducted using the GROMACS package to evaluate dynamic actions and structural stability. The LigandScout was utilized for pharmacophore modeling, which employs a shape-based screening approach to identify potential ligand binding sites on protein targets. RESULTS The molecular docking studies elucidated promising interactions between PMMA and MMA with key biomolecular targets relevant to dental applications. MD simulation results provided strong evidence supporting the structural stability of PMMA complexes over time. Pharmacophore modeling highlighted the significance of carbonyl and hydroxyl groups as pharmacophoric features, indicating compounds with favorable biocompatibility profiles. CONCLUSION This study underscores the potential of PMMA in dental applications, emphasizing its structural stability, molecular interactions, and safety considerations. These findings lay a foundation for future advancements in dental biomaterials, guiding the design and optimization of materials for enhanced biocompatibility. Future directions include experimental validation of computational findings and the development of PMMA-based dental materials with improved biocompatibility and clinical performance.
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Affiliation(s)
- Ravinder S Saini
- Department of Dental Technology, COAMS, King Khalid University, Abha, Saudi Arabia
| | | | | | | | - Shashit Shetty Bavabeedu
- Department of Restorative Dentistry, College of Dentistry, King Khalid University, Abha, Saudi Arabia
| | - Rajesh Vyas
- Department of Dental Technology, COAMS, King Khalid University, Abha, Saudi Arabia
| | - Doni Dermawan
- Department of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | | | - Seyed Ali Mosaddad
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
- Student Research Committee, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Artak Heboyan
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
- Department of Prosthodontics, Faculty of Stomatology, Yerevan State Medical University after Mkhitar Heratsi, Yerevan, Armenia.
- Department of Prosthodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran.
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6
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Islami V, Bittner P, Fiala T, Hentzen NB, Zenobi R, Wennemers H. Self-Sorting Collagen Heterotrimers. J Am Chem Soc 2024; 146:1789-1793. [PMID: 38156954 DOI: 10.1021/jacs.3c12295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Nature uses elaborate methods to control protein assembly, including that of heterotrimeric collagen. Here, we established design principles for the composition and register-selective assembly of synthetic collagen heterotrimers. The assembly code enabled the self-sorting of eight different strands into three─out of 512 possible─triple helices via complementary (4S)-aminoproline and aspartate residues. Native ESI-MS corroborated the specific assembly into coexisting heterotrimers.
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Affiliation(s)
- Valdrin Islami
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Philipp Bittner
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Nina B Hentzen
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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7
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Mohanto S, Narayana S, Merai KP, Kumar JA, Bhunia A, Hani U, Al Fatease A, Gowda BHJ, Nag S, Ahmed MG, Paul K, Vora LK. Advancements in gelatin-based hydrogel systems for biomedical applications: A state-of-the-art review. Int J Biol Macromol 2023; 253:127143. [PMID: 37793512 DOI: 10.1016/j.ijbiomac.2023.127143] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023]
Abstract
A gelatin-based hydrogel system is a stimulus-responsive, biocompatible, and biodegradable polymeric system with solid-like rheology that entangles moisture in its porous network that gradually protrudes to assemble a hierarchical crosslinked arrangement. The hydrolysis of collagen directs gelatin construction, which retains arginyl glycyl aspartic acid and matrix metalloproteinase-sensitive degeneration sites, further confining access to chemicals entangled within the gel (e.g., cell encapsulation), modulating the release of encapsulated payloads and providing mechanical signals to the adjoining cells. The utilization of various types of functional tunable biopolymers as scaffold materials in hydrogels has become highly attractive due to their higher porosity and mechanical ability; thus, higher loading of proteins, peptides, therapeutic molecules, etc., can be further modulated. Furthermore, a stimulus-mediated gelatin-based hydrogel with an impaired concentration of gellan demonstrated great shear thinning and self-recovering characteristics in biomedical and tissue engineering applications. Therefore, this contemporary review presents a concise version of the gelatin-based hydrogel as a conceivable biomaterial for various biomedical applications. In addition, the article has recapped the multiple sources of gelatin and their structural characteristics concerning stimulating hydrogel development and delivery approaches of therapeutic molecules (e.g., proteins, peptides, genes, drugs, etc.), existing challenges, and overcoming designs, particularly from drug delivery perspectives.
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Affiliation(s)
- Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India.
| | - Soumya Narayana
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India
| | - Khushboo Paresh Merai
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujrat, India
| | - Jahanvee Ashok Kumar
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujrat, India
| | - Adrija Bhunia
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Adel Al Fatease
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - B H Jaswanth Gowda
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India; School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast BT9 7BL, UK.
| | - Sagnik Nag
- Department of Bio-Sciences, School of Biosciences & Technology, Vellore Institute of Technology (VIT), Tiruvalam Rd, 632014, Tamil Nadu, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, Karnataka, India
| | - Karthika Paul
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru 570015, Karnataka, India
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast BT9 7BL, UK
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8
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Ahmad S, Sayeed S, Bano N, Sheikh K, Raza K. In-silico analysis reveals Quinic acid as a multitargeted inhibitor against Cervical Cancer. J Biomol Struct Dyn 2023; 41:9770-9786. [PMID: 36379678 DOI: 10.1080/07391102.2022.2146202] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 11/17/2022]
Abstract
The cervix is the lowermost part of the uterus that connects to the vagina, and cervical cancer is a malignant cervix tumour. One of this cancer's most important risk factors is HPV infection. In the approach to finding an effective treatment for this disease, various works have been done around genomics and drug discovery. Finding the major altered genes was one of the most significant studies completed in the field of cervical cancer by TCGA (The Cancer Genome Atlas), and these genes are TGFBR2, MED1, ERBB3, CASP8, and HLA-A. The greatest genomic alterations were found in the PI3K/MAPK and TGF-Beta signalling pathways, suggesting that numerous therapeutic targets may come from these pathways in the future. We, therefore, conducted a combined enrichment analysis of genes gathered from various works of literature for this study. The final six key genes from the list were obtained after enrichment analysis using GO, KEGG, and Reactome methods. The six proteins against the identified genes were then subjected to a docking-based screening against a library of 6,87,843 prepared natural compounds from the ZINC15 database. The most stable compound was subsequently discovered through virtual screening to be the natural substance Quinic acid, which also had the highest binding affinity for all six proteins and a better docking score. To examine their stability, the study was extended to MM/GBSA and MD simulations on the six docked proteins, and comparative docking-based calculations led us to identify the Quinic Acid as a multitargeted compound. The overall deviation of the compound was less than 2 Å for all the complexes considered best for the biological molecules, and the simulation interaction analysis reveals a huge web of interaction during the simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Salwa Sayeed
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Nagmi Bano
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Kayenat Sheikh
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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9
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Boudko SP, Konopka EH, Kim W, Taga Y, Mizuno K, Springer TA, Hudson BG, Moy TI, Lin FY. A recombinant technique for mapping functional sites of heterotrimeric collagen helices: Collagen IV CB3 fragment as a prototype for integrin binding. J Biol Chem 2023; 299:104901. [PMID: 37302550 PMCID: PMC10404678 DOI: 10.1016/j.jbc.2023.104901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
Collagen superfamily of proteins is a major component of the extracellular matrix. Defects in collagens underlie the cause of nearly 40 human genetic diseases in millions of people worldwide. Pathogenesis typically involves genetic alterations of the triple helix, a hallmark structural feature that bestows exceptional mechanical resistance to tensile forces and a capacity to bind a plethora of macromolecules. Yet, there is a paramount knowledge gap in understanding the functionality of distinct sites along the triple helix. Here, we present a recombinant technique to produce triple helical fragments for functional studies. The experimental strategy utilizes the unique capacity of the NC2 heterotrimerization domain of collagen IX to drive three α-chain selection and registering the triple helix stagger. For proof of principle, we produced and characterized long triple helical fragments of collagen IV that were expressed in a mammalian system. The heterotrimeric fragments encompassed the CB3 trimeric peptide of collagen IV, which harbors the binding motifs for α1β1 and α2β1 integrins. Fragments were characterized and shown to have a stable triple helix, post-translational modifications, and high affinity and specific binding of integrins. The NC2 technique is a universal tool for the high-yield production of heterotrimeric fragments of collagens. Fragments are suitable for mapping functional sites, determining coding sequences of binding sites, elucidating pathogenicity and pathogenic mechanisms of genetic mutations, and production of fragments for protein replacement therapy.
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Affiliation(s)
- Sergei P Boudko
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
| | | | - Woojin Kim
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Yuki Taga
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Kazunori Mizuno
- Nippi Research Institute of Biomatrix, Toride, Ibaraki, Japan
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Billy G Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Terence I Moy
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA
| | - Fu-Yang Lin
- Morphic Therapeutic, Inc, Waltham, Massachusetts, USA.
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10
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Yu LT, Hancu MC, Kreutzberger MAB, Henrickson A, Demeler B, Egelman EH, Hartgerink JD. Hollow Octadecameric Self-Assembly of Collagen-like Peptides. J Am Chem Soc 2023; 145:5285-5296. [PMID: 36812303 PMCID: PMC10131286 DOI: 10.1021/jacs.2c12931] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The folding of collagen is a hierarchical process that starts with three peptides associating into the characteristic triple helical fold. Depending on the specific collagen in question, these triple helices then assemble into bundles reminiscent of α-helical coiled-coils. Unlike α-helices, however, the bundling of collagen triple helices is very poorly understood with almost no direct experimental data available. In order to shed light on this critical step of collagen hierarchical assembly, we have examined the collagenous region of complement component 1q. Thirteen synthetic peptides were prepared to dissect the critical regions allowing for its octadecameric self-assembly. We find that short peptides (under 40 amino acids) are able to self-assemble into specific (ABC)6 octadecamers. This requires the ABC heterotrimeric composition as the self-assembly subunit, but does not require disulfide bonds. Self-assembly into this octadecamer is aided by short noncollagenous sequences at the N-terminus, although they are not entirely required. The mechanism of self-assembly appears to begin with the very slow formation of the ABC heterotrimeric helix, followed by rapid bundling of triple helices into progressively larger oligomers, terminating in the formation of the (ABC)6 octadecamer. Cryo-electron microscopy reveals the (ABC)6 assembly as a remarkable, hollow, crown-like structure with an open channel approximately 18 Å at the narrow end and 30 Å at the wide end. This work helps to illuminate the structure and assembly mechanism of a critical protein in the innate immune system and lays the groundwork for the de novo design of higher order collagen mimetic peptide assemblies.
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Affiliation(s)
- Le Tracy Yu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, United States
| | - Maria C. Hancu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, United States
| | - Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia Box 800733, Charlottesville, VA 22908, United States
| | - Amy Henrickson
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia Box 800733, Charlottesville, VA 22908, United States
| | - Jeffrey D. Hartgerink
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, United States
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11
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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12
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Kim SC, Heo SY, Oh GW, Yi M, Jung WK. A 3D-Printed Polycaprolactone/Marine Collagen Scaffold Reinforced with Carbonated Hydroxyapatite from Fish Bones for Bone Regeneration. Mar Drugs 2022; 20:md20060344. [PMID: 35736147 PMCID: PMC9230561 DOI: 10.3390/md20060344] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
In bone tissue regeneration, extracellular matrix (ECM) and bioceramics are important factors, because of their osteogenic potential and cell–matrix interactions. Surface modifications with hydrophilic material including proteins show significant potential in tissue engineering applications, because scaffolds are generally fabricated using synthetic polymers and bioceramics. In the present study, carbonated hydroxyapatite (CHA) and marine atelocollagen (MC) were extracted from the bones and skins, respectively, of Paralichthys olivaceus. The extracted CHA was characterized using Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) analysis, while MC was characterized using FTIR spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The scaffolds consisting of polycaprolactone (PCL), and different compositions of CHA (2.5%, 5%, and 10%) were fabricated using a three-axis plotting system and coated with 2% MC. Then, the MC3T3-E1 cells were seeded on the scaffolds to evaluate the osteogenic differentiation in vitro, and in vivo calvarial implantation of the scaffolds was performed to study bone tissue regeneration. The results of mineralization confirmed that the MC/PCL, 2.5% CHA/MC/PCL, 5% CHA/MC/PCL, and 10% CHA/MC/PCL scaffolds increased osteogenic differentiation by 302%, 858%, 970%, and 1044%, respectively, compared with pure PCL scaffolds. Consequently, these results suggest that CHA and MC obtained from byproducts of P. olivaceus are superior alternatives for land animal-derived substances.
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Affiliation(s)
- Se-Chang Kim
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence and New-Senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48531, Korea; (S.-C.K.); (M.Y.)
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Korea
| | - Seong-Yeong Heo
- Jeju Marine Research Center, Korea Institute of Ocean Science & Technology (KIOST), Jeju 63349, Korea;
| | - Gun-Woo Oh
- National Marine Biodiversity Institute of Korea (MABIK), Seochun, Chungcheongnam 33662, Korea;
| | - Myunggi Yi
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence and New-Senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48531, Korea; (S.-C.K.); (M.Y.)
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Korea
| | - Won-Kyo Jung
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence and New-Senior Healthcare Innovation Center (BK21 Plus), Pukyong National University, Busan 48531, Korea; (S.-C.K.); (M.Y.)
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Korea
- Correspondence: ; Tel.: +82-51-629-5775
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13
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Picker J, Lan Z, Arora S, Green M, Hahn M, Cosgriff-Hernandez E, Hook M. Prokaryotic Collagen-Like Proteins as Novel Biomaterials. Front Bioeng Biotechnol 2022; 10:840939. [PMID: 35372322 PMCID: PMC8968730 DOI: 10.3389/fbioe.2022.840939] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 12/13/2022] Open
Abstract
Collagens are the major structural component in animal extracellular matrices and are critical signaling molecules in various cell-matrix interactions. Its unique triple helical structure is enabled by tripeptide Gly-X-Y repeats. Understanding of sequence requirements for animal-derived collagen led to the discovery of prokaryotic collagen-like protein in the early 2000s. These prokaryotic collagen-like proteins are structurally similar to mammalian collagens in many ways. However, unlike the challenges associated with recombinant expression of mammalian collagens, these prokaryotic collagen-like proteins can be readily expressed in E. coli and are amenable to genetic modification. In this review article, we will first discuss the properties of mammalian collagen and provide a comparative analysis of mammalian collagen and prokaryotic collagen-like proteins. We will then review the use of prokaryotic collagen-like proteins to both study the biology of conventional collagen and develop a new biomaterial platform. Finally, we will describe the application of Scl2 protein, a streptococcal collagen-like protein, in thromboresistant coating for cardiovascular devices, scaffolds for bone regeneration, chronic wound dressing and matrices for cartilage regeneration.
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Affiliation(s)
- Jonathan Picker
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M, Houston, TX, United States
| | - Ziyang Lan
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M, Houston, TX, United States
| | - Mykel Green
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Mariah Hahn
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, United States
| | | | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M, Houston, TX, United States
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14
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Yu LT, Hartgerink JD. Selective covalent capture of collagen triple helices with a minimal protecting group strategy. Chem Sci 2022; 13:2789-2796. [PMID: 35356674 PMCID: PMC8890135 DOI: 10.1039/d1sc06361h] [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: 11/16/2021] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
A minimal protecting group strategy is developed to allow selective covalent capture of collagen-like triple helices. This allows stabilization of this critical fold while preserving charge–pair interactions critical for biological applications.
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Affiliation(s)
- Le Tracy Yu
- Rice University, Department of Chemistry and Department of Bioengineering, Houston, TX 77005, USA
| | - Jeffrey D. Hartgerink
- Rice University, Department of Chemistry and Department of Bioengineering, Houston, TX 77005, USA
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15
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Arora S, Gordon J, Hook M. Collagen Binding Proteins of Gram-Positive Pathogens. Front Microbiol 2021; 12:628798. [PMID: 33613497 PMCID: PMC7893114 DOI: 10.3389/fmicb.2021.628798] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
Collagens are the primary structural components of mammalian extracellular matrices. In addition, collagens regulate tissue development, regeneration and host defense through interaction with specific cellular receptors. Their unique triple helix structure, which requires a glycine residue every third amino acid, is the defining structural feature of collagens. There are 28 genetically distinct collagens in humans. In addition, several other unrelated human proteins contain a collagen domain. Gram-positive bacteria of the genera Staphylococcus, Streptococcus, Enterococcus, and Bacillus express cell surface proteins that bind to collagen. These proteins of Gram-positive pathogens are modular proteins that can be classified into different structural families. This review will focus on the different structural families of collagen binding proteins of Gram-positive pathogen. We will describe how these proteins interact with the triple helix in collagens and other host proteins containing a collagenous domain and discuss how these interactions can contribute to the pathogenic processes.
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Affiliation(s)
- Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
| | - Jay Gordon
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States
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16
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Gonti S, Westler WM, Miyagi M, Bann JG. Site-Specific Labeling and 19F NMR Provide Direct Evidence for Dynamic Behavior of the Anthrax Toxin Pore ϕ-Clamp Structure. Biochemistry 2021; 60:643-647. [PMID: 33428379 DOI: 10.1021/acs.biochem.0c00833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The anthrax toxin protective antigen (PA), the membrane binding and pore-forming component of the anthrax toxin, was studied using 19F NMR. We site-specifically labeled PA with p-fluorophenylalanine (pF-Phe) at Phe427, a critically important residue that comprises the ϕ-clamp that is required for translocation of edema factor (EF) and lethal factor (LF) into the host cell cytosol. We utilized 19F NMR to follow low-pH-induced structural changes in the prepore, alone and bound to the N-terminal PA binding domain of LF, LFN. Our studies indicate that pF-Phe427 is dynamic in the prepore state and then becomes more dynamic in the transition to the pore. An increase in dynamic behavior at the ϕ-clamp may provide the necessary room for movement needed in translocating EF and LF into the cell cytosol.
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Affiliation(s)
- Srinivas Gonti
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - William M Westler
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, United States
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - James G Bann
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
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17
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Fouët G, Bally I, Signor L, Häußermann K, Thielens NM, Rossi V, Gaboriaud C. Headless C1q: a new molecular tool to decipher its collagen-like functions. FEBS J 2020; 288:2030-2041. [PMID: 32869492 DOI: 10.1111/febs.15543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/20/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
Complement component C1q, a soluble defense collagen, is the recognition protein of the classical complement pathway. C1q is able to recognize and interact with multiple targets and, via the subsequent activation of its cognate serine proteases C1r and C1s, initiates the complement cascade. C1q is made up of six ABC heterotrimers each containing two different functional regions, an N-terminal collagen-like region (CLR) and a C-terminal globular region (GR). These heterotrimers assemble via their N-terminal regions, resulting in the characteristic 'bouquet-like' shape of C1q with an N-terminal bundle of collagen fibers with six diverging stems each exhibiting a C-terminal globular head. The GRs are responsible for the versatile recognition of multiple C1q targets, whereas the CLRs trigger immune response through interacting with several cellular or soluble partners. We report here the generation of the first recombinant form of human C1q without its recognition globular heads. The noncollagenous domain 2 (nc2) of type IX collagen has been substituted for the C1q GR in order to control the correct registering of the collagen triple helices of C1q chains A, B, and C. The resulting CLR_nc2 recombinant protein produced in stably transfected EXPI293 mammalian cells was correctly assembled and folded, as demonstrated by mass spectrometry, mass photometry, and electron microscopy experiments. Its interaction properties were investigated using surface plasmon resonance analysis with known CLR ligands: the tetramer of C1r and C1s dimers and MBL-associated protein MAp44. Comparison with the interaction properties of native serum-derived C1q and CLR revealed that recombinant CLR_nc2 retains C1q CLR functional properties.
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Affiliation(s)
| | - Isabelle Bally
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble, France
| | - Luca Signor
- CEA, CNRS, IBS, Université Grenoble Alpes, Grenoble, France
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18
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Hentzen NB, Islami V, Köhler M, Zenobi R, Wennemers H. A Lateral Salt Bridge for the Specific Assembly of an ABC-Type Collagen Heterotrimer. J Am Chem Soc 2020; 142:2208-2212. [DOI: 10.1021/jacs.9b13037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Nina B. Hentzen
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Valdrin Islami
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Martin Köhler
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland
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19
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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20
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New Aspects Towards a Molecular Understanding of the Allicin Immunostimulatory Mechanism via Colec12, MARCO, and SCARB1 Receptors. Int J Mol Sci 2019; 20:ijms20153627. [PMID: 31344978 PMCID: PMC6696194 DOI: 10.3390/ijms20153627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
The allicin pleiotropic effects, which include anti-inflammatory, anti-oxidant, anti-tumoral, and antibacterial actions, were well demonstrated and correlated with various molecular pathways. The immunostimulatory mechanism of allicin has not been elucidated; however, there is a possible cytokine stimulation from immunoglobulin release caused by allicin. In this study, when Wistar female rats and CD19+ lymphocytes were treated with three different doses of allicin, immunoglobulins, glutathione, and oxidative stress markers were assayed. Molecular docking was performed between S-allylmercaptoglutathione (GSSA)—a circulating form of allicin in in vivo systems formed by the allicin interaction with glutathione (GSH)—and scavenger receptors class A and B from macrophages, as well as CD19+ B lymphocytes. Our data demonstrated a humoral immunostimulatory effect of allicin in rats and direct stimulation of B lymphocytes by S-allyl-mercapto-glutathione, both correlated with decreased catalase (CAT) activity. The molecular docking revealed that S-allyl-mercapto-glutathione interacting with Colec12, MARCO (class A), and SCARB1 (class B) scavenger receptors in in vitro tests demonstrates a direct stimulation of immunoglobulin secretion by GSSA in CD19+ B lymphocytes. These data collectively indicate that GSSA stimulates immunoglobulin secretion by binding on scavenger receptors class B type 1 (SCARB1) from CD19+ B lymphocytes.
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21
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22
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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: 4.0] [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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23
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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: 37] [Impact Index Per Article: 5.3] [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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24
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Tang L, Zeng J, Geng P, Fang C, Wang Y, Sun M, Wang C, Wang J, Yin P, Hu C, Guo L, Yu J, Gao P, Li E, Zhuang Z, Xu G, Liu Y. Global Metabolic Profiling Identifies a Pivotal Role of Proline and Hydroxyproline Metabolism in Supporting Hypoxic Response in Hepatocellular Carcinoma. Clin Cancer Res 2018; 24:474-485. [PMID: 29084919 DOI: 10.1158/1078-0432.ccr-17-1707] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/02/2017] [Accepted: 10/24/2017] [Indexed: 01/13/2023]
Abstract
Purpose: Metabolic reprogramming is frequently identified in hepatocellular carcinoma (HCC), which is the most common type of liver malignancy. The reprogrammed cellular metabolisms promote tumor cell survival, proliferation, angiogenesis, and metastasis. However, the mechanisms of this process remain unclear in HCC.Experimental Design: The global nontargeted metabolic study in 69 paired hepatic carcinomas and adjacent tissue specimens was performed using capillary electrophoresis-time of flight mass spectrometry-based approach. Key findings were validated by targeted metabolomic approach. Biological studies were also performed to investigate the role of proline biosynthesis in HCC pathogenesis.Results: Proline metabolism was markedly changed in HCC tumor tissue, characterized with accelerated consumption of proline and accumulation of hydroxyproline, which significantly correlated with α-fetoprotein levels and poor prognosis in HCC. In addition, we found that hydroxyproline promoted hypoxia- and HIF-dependent phenotype in HCC. Moreover, we demonstrated that hypoxia activated proline biosynthesis via upregulation of ALDH18A1, subsequently leading to accumulation of hydroxyproline via attenuated PRODH2 activity. More importantly, we showed that glutamine, proline, and hydroxyproline metabolic axis supported HCC cell survival through modulating HIF1α stability in response to hypoxia. Finally, inhibition of proline biosynthesis significantly enhanced cytotoxicity of sorafenib in vitro and in vivoConclusions: Our results demonstrate that hypoxic microenvironment activates proline metabolism, resulting in accumulation of hydroxyproline that promotes HCC tumor progression and sorafenib resistance through modulating HIF1α. These findings provide the proof of concept for targeting proline metabolism as a potential therapeutic strategy for HCC. Clin Cancer Res; 24(2); 474-85. ©2017 AACR.
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Affiliation(s)
- Ling Tang
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- School of Life Science, Dalian University, Dalian, China
| | - Jun Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Dalian, China
| | - Pengyu Geng
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chengnan Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yang Wang
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- School of Life Science, Dalian University, Dalian, China
| | - Mingju Sun
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Changsong Wang
- Department of Anesthesiology, First Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Critical Care Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiao Wang
- School of Life Science, Dalian University, Dalian, China
| | - Peiyuan Yin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lei Guo
- Department of Anesthesiology, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jane Yu
- Division of Pulmonary, Critical Care and Sleep Medicine Department of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Peng Gao
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Enyou Li
- Department of Anesthesiology, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhengping Zhuang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Yang Liu
- Scientific Research Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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25
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Egli J, Siebler C, Maryasin B, Erdmann RS, Bergande C, Ochsenfeld C, Wennemers H. pH-Responsive Aminoproline-Containing Collagen Triple Helices. Chemistry 2017; 23:7938-7944. [DOI: 10.1002/chem.201701134] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christiane Siebler
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Boris Maryasin
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Roman S. Erdmann
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Cedric Bergande
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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26
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Sharma U, Carrique L, Vadon-Le Goff S, Mariano N, Georges RN, Delolme F, Koivunen P, Myllyharju J, Moali C, Aghajari N, Hulmes DJS. Structural basis of homo- and heterotrimerization of collagen I. Nat Commun 2017; 8:14671. [PMID: 28281531 PMCID: PMC5353611 DOI: 10.1038/ncomms14671] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
Fibrillar collagen molecules are synthesized as precursors, procollagens, with large propeptide extensions. While a homotrimeric form (three α1 chains) has been reported in embryonic tissues as well as in diseases (cancer, fibrosis, genetic disorders), collagen type I usually occurs as a heterotrimer (two α1 chains and one α2 chain). Inside the cell, the role of the C-terminal propeptides is to gather together the correct combination of three α chains during molecular assembly, but how this occurs for different forms of the same collagen type is so far unknown. Here, by structural and mutagenic analysis, we identify key amino acid residues in the α1 and α2 C-propeptides that determine homo- and heterotrimerization. A naturally occurring mutation in one of these alters the homo/heterotrimer balance. These results show how the C-propeptide of the α2 chain has specifically evolved to permit the appearance of heterotrimeric collagen I, the major extracellular building block among the metazoa.
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Affiliation(s)
- Urvashi Sharma
- Molecular Microbiology and Structural Biochemistry Unit, UMR 5086 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Loïc Carrique
- Molecular Microbiology and Structural Biochemistry Unit, UMR 5086 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Sandrine Vadon-Le Goff
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Natacha Mariano
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Rainier-Numa Georges
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Frederic Delolme
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France.,SFR Biosciences - Protein Science Facility, University of Lyon 1, Ecole Normale Supérieure de Lyon, INSERM US8, CNRS UMS 3444, 50 Avenue Tony Garnier, F-69366 Lyon, France
| | - Peppi Koivunen
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5000, FI-90014 Oulu, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5000, FI-90014 Oulu, Finland
| | - Catherine Moali
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry Unit, UMR 5086 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
| | - David J S Hulmes
- Tissue Biology and Therapeutic Engineering Unit, UMR 5305 CNRS - University of Lyon 1, 7 passage du Vercors, F-69367 Lyon, France
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27
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Egli J, Erdmann RS, Schmidt PJ, Wennemers H. Effect of N- and C-terminal functional groups on the stability of collagen triple helices. Chem Commun (Camb) 2017; 53:11036-11039. [DOI: 10.1039/c7cc05837c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effect of chargedversusneutral N- and C-termini on the stability of the collagen triple helix was examined.
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Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry
- D-CHAB
- ETH Zurich, Vladimir-Prelog-Weg 3
- CH-8093 Zurich
- Switzerland
| | - Roman S. Erdmann
- Laboratory of Organic Chemistry
- D-CHAB
- ETH Zurich, Vladimir-Prelog-Weg 3
- CH-8093 Zurich
- Switzerland
| | - Pascal J. Schmidt
- Laboratory of Organic Chemistry
- D-CHAB
- ETH Zurich, Vladimir-Prelog-Weg 3
- CH-8093 Zurich
- Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry
- D-CHAB
- ETH Zurich, Vladimir-Prelog-Weg 3
- CH-8093 Zurich
- Switzerland
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