1
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Meshcheryakova OV, Bogdanov MA, Efimov AV. Relationship between thermal stability of collagens and the fraction of hydrophobic residues in their molecules. J Struct Biol 2024; 216:108114. [PMID: 39094716 DOI: 10.1016/j.jsb.2024.108114] [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: 05/23/2024] [Revised: 07/18/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
In this study, a database of the thermal stability of collagens and their synthetic analogues has been compiled taking into account literature sources. In total, our database includes 1200 records. As a result of a comparative theoretical analysis of the collected experimental data, the relationship between the melting temperature (Tm) or denaturation temperature (Td) of collagens and the fraction of hydrophobic residues (f) in their molecules has been established. It is shown that this relationship is linear: the larger the f value, the higher the denaturation or melting temperature of a given collagen.
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Affiliation(s)
- Olga V Meshcheryakova
- Centre for Biomedical Research of the Karelian Research Centre of the Russian Academy of Sciences, Pushkinskaya St., 11, Petrozavodsk 185910 Russia.
| | - Maxim A Bogdanov
- Laboratory of Intellectual Services and Applications, ITMO University, Kronverksky Pr., 49, St.Petersburg 197101, Russia
| | - Alexander V Efimov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya St., 4, Pushchino, Moscow Region 142290 Russia.
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2
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Torrez M, Brajanovska A, Slowinska K. Selective Excitation of the 1L α State of Tryptophan in Collagen-like Peptides Can Reveal the Formation of a Heterotrimer. ACS OMEGA 2024; 9:29848-29856. [PMID: 39005791 PMCID: PMC11238237 DOI: 10.1021/acsomega.4c03600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024]
Abstract
Fluorescence emission from tryptophan residues has been often used to probe the protein structure due to its transition dipole moment sensitivity to the local environment. We report the fluorescence study of a collagen-like peptide heterotrimer modified with the tryptophan in the X position (X-Y-Gly) n that shows the diminished fluorescence in a homotrimer versus a heterotrimer when the 1Lα state is selectively excited. This behavior is only observed in folded peptides, below the helix-to-coil transition temperature, and can be explained by long-range interactions between the tryptophans located on different strands within the triple helix, not by the change in the local environment. Our results suggest that tryptophan homotransfer is possible at distances much longer than the R 0 (0.5-0.7 nm) previously estimated. These observations imply that the energy transfer between the 1Lα states of proximal tryptophans can be facilitated by constraining their rotation by the helix and, thus, can be employed as a reporter of heterotrimer formation in biosensors.
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Affiliation(s)
- Miriam Torrez
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, California 90840, United States
| | - Aleksandra Brajanovska
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, California 90840, United States
| | - Katarzyna Slowinska
- Department of Chemistry and Biochemistry, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, California 90840, United States
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3
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Selvaraj V, Sekaran S, Dhanasekaran A, Warrier S. Type 1 collagen: Synthesis, structure and key functions in bone mineralization. Differentiation 2024; 136:100757. [PMID: 38437764 DOI: 10.1016/j.diff.2024.100757] [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: 09/30/2023] [Revised: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
Collagen is a highly abundant protein in the extracellular matrix of humans and mammals, and it plays a critical role in maintaining the body's structural integrity. Type I collagen is the most prevalent collagen type and is essential for the structural integrity of various tissues. It is present in nearly all connective tissues and is the main constituent of the interstitial matrix. Mutations that affect collagen fiber formation, structure, and function can result in various bone pathologies, underscoring the significance of collagen in sustaining healthy bone tissue. Studies on type 1 collagen have revealed that mutations in its encoding gene can lead to diverse bone diseases, such as osteogenesis imperfecta, a disorder characterized by fragile bones that are susceptible to fractures. Knowledge of collagen's molecular structure, synthesis, assembly, and breakdown is vital for comprehending embryonic and foetal development and several aspects of human physiology. In this review, we summarize the structure, molecular biology of type 1 collagen, its biomineralization and pathologies affecting bone.
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Affiliation(s)
- Vimalraj Selvaraj
- Department of Applied Mechanics and Biomedical Engineering, Indian Institute of Technology-Madras, Chennai, 600 036, Tamil Nadu, India.
| | - Saravanan Sekaran
- Department of Prosthodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, Tamil Nadu, India.
| | | | - Sudha Warrier
- Department of Biotechnology, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, Tamil Nadu, India
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4
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Nomura K, Fiala T, Wennemers H. Carbohydrate Co-Solutes Stabilize Collagen Triple Helices. Chembiochem 2024; 25:e202300860. [PMID: 38233350 DOI: 10.1002/cbic.202300860] [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: 12/21/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Carbohydrates are common co-solutes for the stabilization of proteins. The effect of carbohydrate solutions on the stability of collagen, the most abundant protein in mammals, is, however, underexplored. In this work, we studied the thermal stability of collagen triple helices derived from a molecularly defined collagen model peptide (CMP), Ac-(Pro-Hyp-Gly)7 -NH2 , in solutions of six common mono- and disaccharides. We show that the carbohydrates stabilize the collagen triple helix in a concentration-dependent manner, with an increase of the melting temperature of up to 17 °C. In addition, we show that the stabilizing effect is similar for all studied sugars, including trehalose, which is otherwise considered a privileged bioprotectant. The results provided insight into the effects of sugar co-solutes on collagen triple helices and can aid the selection of storage environments for collagen-based materials and probes.
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Affiliation(s)
- Kota Nomura
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Tomas Fiala
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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5
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Campbell L, Fredericks J, Mathivha K, Moshesh P, Coovadia A, Chirwa P, Dillon B, Ghoor A, Lawrence D, Nair L, Mabaso N, Mokwele D, Novellie M, Krause A, Carstens N. The implementation and utility of clinical exome sequencing in a South African infant cohort. Front Genet 2023; 14:1277948. [PMID: 38028619 PMCID: PMC10665497 DOI: 10.3389/fgene.2023.1277948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.
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Affiliation(s)
- L. Campbell
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J. Fredericks
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - K. Mathivha
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Moshesh
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson Mandela Children’s Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Coovadia
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - P. Chirwa
- Nelson Mandela Children’s Hospital, Johannesburg, South Africa
| | - B. Dillon
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Ghoor
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Lawrence
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Nair
- Department of Paediatrics and Child Health, School of Clinical Medicine, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Mabaso
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - D. Mokwele
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Novellie
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. Krause
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - N. Carstens
- Division of Human Genetics, National Health Laboratory Service andSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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6
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Fiala T, Heeb R, Vigliotti L, Wennemers H. The Yin and Yang of How N-Terminal Acyl Caps Affect Collagen Triple Helices. Biomacromolecules 2023; 24:3954-3960. [PMID: 37227696 DOI: 10.1021/acs.biomac.3c00241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
N-terminal acylation is a common tool for the installation of functional moieties (e.g., sensors or bioactive molecules) on collagen model peptides (CMPs). The N-acyl group and its length are generally assumed to have little or no influence on the properties of the collagen triple helix formed by the CMP. Here, we show that the length of short (C1-C4) acyl capping groups has different effects on the thermal stability of collagen triple helices in POG, OGP, and GPO frames. While the effect of different capping groups on the stability of triple helices in the GPO frame is negligible, longer acyl chains stabilize OGP triple helices but destabilize POG analogues. The observed trends arise from a combination of steric repulsion, the hydrophobic effect, and n → π* interactions. Our study provides a basis for the design of N-terminally functionalized CMPs with predictable effects on triple helix stability.
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Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Rahel Heeb
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Luca Vigliotti
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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7
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Keever JM, Banzon PD, Hales MK, Sargent AL, Allen WE. Association between N-Terminal Pyrenes Stabilizes the Collagen Triple Helix. J Org Chem 2023; 88:11885-11894. [PMID: 37531574 DOI: 10.1021/acs.joc.3c01175] [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: 08/04/2023]
Abstract
Collagen model peptides featuring the fluorophore pyrene at their N-termini have been synthesized, and their thermal denaturation has been examined using circular dichroism (CD) and fluorescence spectroscopies. Flanking the (Pro-Hyp-Gly)7 core of the peptide monomers at positions 1 and/or 23 in the primary sequence, Lys residues were introduced to ensure water solubility. Triple helices derived from such peptides show a broad excimer emission at ∼480 nm, indicative of interaction between the pyrene units. CD experiments show that the fluorophores enhance helix stability primarily through entropic effects. Unfolding temperatures (Tm) increase by up to 7 °C for systems with N-terminal lysine residues and by up to 21 °C for systems in which the first-position Lys is replaced by Ala. Tm values derived from fluorescence measurements (at 50 μM) typically lie within ∼1 °C of those obtained using CD (at 200 μM). Computational modeling in a water continuum using B3LYP-GD3 and M06-2X functionals predicts that face-to-face association of fluorophores can occur while H-bonding within the [(POG)n]3 assembly is retained. Such parallel stacking is consistent with hydrophobically driven stabilization. Labeling collagen peptides with pyrene is a synthetically simple way to promote triple helicity while providing a means to obtain Tm data on relatively dilute samples.
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Affiliation(s)
- Jared M Keever
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Patrick D Banzon
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Megan K Hales
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - Andrew L Sargent
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
| | - William E Allen
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, North Carolina 27858-4353, United States
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8
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Fiala T, Barros EP, Heeb R, Riniker S, Wennemers H. Predicting Collagen Triple Helix Stability through Additive Effects of Terminal Residues and Caps. Angew Chem Int Ed Engl 2023; 62:e202214728. [PMID: 36409045 PMCID: PMC10108146 DOI: 10.1002/anie.202214728] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Collagen model peptides (CMPs) consisting of proline-(2S,4R)-hydroxyproline-glycine (POG) repeats have provided a breadth of knowledge of the triple helical structure of collagen, the most abundant protein in mammals. Predictive tools for triple helix stability have, however, lagged behind since the effect of CMPs with different frames ([POG]n , [OGP]n , or [GPO]n ) and capped or uncapped termini have so far been underestimated. Here, we elucidated the impact of the frame, terminal functional group and its charge on the stability of collagen triple helices. Combined experimental and theoretical studies with frame-shifted, capped and uncapped CMPs revealed that electrostatic interactions, strand preorganization, interstrand H-bonding, and steric repulsion at the termini contribute to triple helix stability. We show that these individual contributions are additive and allow for the prediction of the melting temperatures of CMP trimers.
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Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Emilia P Barros
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Rahel Heeb
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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9
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Hierarchical Structure and Properties of the Bone at Nano Level. Bioengineering (Basel) 2022; 9:bioengineering9110677. [PMID: 36354587 PMCID: PMC9687701 DOI: 10.3390/bioengineering9110677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
Bone is a highly hierarchical complex structure that consists of organic and mineral components represented by collagen molecules (CM) and hydroxyapatite crystals (HAC), respectively. The nanostructure of bone can significantly affect its mechanical properties. There is a lack of understanding how collagen fibrils (CF) in different orientations may affect the mechanical properties of the bone. The objective of this study is to investigate the effect of interaction, orientation, and hydration on atomic models of the bone composed of collagen helix (CH) and HAC, using molecular dynamics simulations and therefrom bone-related disease origins. The results demonstrate that the mechanical properties of the bone are affected significantly by the orientation of the CF attributed to contact areas at 0° and 90° models. The molecular dynamics simulation illustrated that there is significant difference (p < 0.005) in the ultimate tensile strength and toughness with respect to the orientation of the hydrated and un-hydrated CF. Additionally, the results indicated that having the force in a longitudinal direction (0°) provides more strength compared with the CF in the perpendicular direction (90°). Furthermore, the results show that substituting glycine (GLY) with any other amino acid affects the mechanical properties and strength of the CH, collagen−hydroxyapatite interface, and eventually affects the HAC. Generally, hydration dramatically influences bone tissue elastic properties, and any change in the orientation or any abnormality in the atomic structure of either the CM or the HAC would be the main reason of the fragility in the bone, affecting bone pathology.
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10
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Zhang R, Xu Y, Lan J, Fan S, Huang J, Xu F. Structural Achievability of an NH-π Interaction between Gln and Phe in a Crystal Structure of a Collagen-like Peptide. Biomolecules 2022; 12:1433. [PMID: 36291642 PMCID: PMC9599227 DOI: 10.3390/biom12101433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
NH-π interactions between polar and aromatic residues are well distributed in proteins whose stabilizing effects have been investigated in globular and fibrous proteins. In order to gain structural insights into side chain NH-π interactions, we solved a crystal structure of a collagen-like peptide containing Gln-Phe pairs. The Gln-Phe NH-π interactions were further characterized by quantum calculations, molecular simulations, and structural bioinformatics. The analyses indicated that the NH-π interactions are robust under various solvent conditions, can be distributed either on the protein surface or in its hydrophobic core and can form at a wide range of distances between residues. This study suggested that NH-π interactions can play a versatile role in protein design, including engineering hydrophobic cores, solvent accessible surfaces, and protein-protein interfaces.
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Affiliation(s)
- Ruixue Zhang
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - You Xu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Jun Lan
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shilong Fan
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
| | - Fei Xu
- Ministry of Education Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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11
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Rani A, Sindhu A, Yao TJ, Horng JC, Venkatesu P. Profiling the impact of choline chloride on the self-assembly of collagen mimetic peptide (Pro-Hyp-Gly)10. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Khare E, Gonzalez-Obeso C, Kaplan DL, Buehler MJ. CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach. ACS Biomater Sci Eng 2022; 8:4301-4310. [PMID: 36149671 DOI: 10.1021/acsbiomaterials.2c00737] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen is one of the most important structural proteins in biology, and its structural hierarchy plays a crucial role in many mechanically important biomaterials. Here, we demonstrate how transformer models can be used to predict, directly from the primary amino acid sequence, the thermal stability of collagen triple helices, measured via the melting temperature Tm. We report two distinct transformer architectures to compare performance. First, we train a small transformer model from scratch, using our collagen data set featuring only 633 sequence-to-Tm pairings. Second, we use a large pretrained transformer model, ProtBERT, and fine-tune it for a particular downstream task by utilizing sequence-to-Tm pairings, using a deep convolutional network to translate natural language processing BERT embeddings into required features. Both the small transformer model and the fine-tuned ProtBERT model have similar R2 values of test data (R2 = 0.84 vs 0.79, respectively), but the ProtBERT is a much larger pretrained model that may not always be applicable for other biological or biomaterials questions. Specifically, we show that the small transformer model requires only 0.026% of the number of parameters compared to the much larger model but reaches almost the same accuracy for the test set. We compare the performance of both models against 71 newly published sequences for which Tm has been obtained as a validation set and find reasonable agreement, with ProtBERT outperforming the small transformer model. The results presented here are, to our best knowledge, the first demonstration of the use of transformer models for relatively small data sets and for the prediction of specific biophysical properties of interest. We anticipate that the work presented here serves as a starting point for transformer models to be applied to other biophysical problems.
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Affiliation(s)
- Eesha Khare
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | | | - David L Kaplan
- Tufts University, Medford, Massachusetts 02155, United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States.,Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
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13
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Lee B, Jaberi-Lashkari N, Calo E. A unified view of low complexity regions (LCRs) across species. eLife 2022; 11:e77058. [PMID: 36098382 PMCID: PMC9470157 DOI: 10.7554/elife.77058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
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Affiliation(s)
- Byron Lee
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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14
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Qiang S, Lu C, Xu F. Disrupting Effects of Osteogenesis Imperfecta Mutations Could Be Predicted by Local Hydrogen Bonding Energy. Biomolecules 2022; 12:biom12081104. [PMID: 36008998 PMCID: PMC9405839 DOI: 10.3390/biom12081104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Osteogenesis imperfecta(OI) is a disease caused by substitution in glycine residues with different amino acids in type I collagen (Gly-Xaa-Yaa)n. Collagen model peptides can capture the thermal stability loss of the helix after Gly mutations, most of which are homotrimers. However, a majority of natural collagen exists in heterotrimers. To investigate the effects of chain specific mutations in the natural state of collagen more accurately, here we introduce various lengths of side-chain amino acids into ABC-type heterotrimers. The disruptive effects of the mutations were characterized both experimentally and computationally. We found the stability decrease in the mutants was mainly caused by the disruption of backbone hydrogen bonds. Meanwhile, we found a threshold value of local hydrogen bonding energy that could predict triple helix folding or unfolding. Val caused the unfolding of triple helices, whereas Ser with a similar side-chain length did not. Structural details suggested that the side-chain hydroxyl group in Ser forms hydrogen bonds with the backbone, thereby compensating for the mutants’ decreased stability. Our study contributes to a better understanding of how OI mutations destabilize collagen triple helices and the molecular mechanisms underlying OI.
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Nadyrshina D, Zaripova A, Tyurin A, Minniakhmetov I, Zakharova E, Khusainova R. Osteogenesis Imperfecta: Search for Mutations in Patients from the Republic of Bashkortostan (Russia). Genes (Basel) 2022; 13:genes13010124. [PMID: 35052464 PMCID: PMC8774438 DOI: 10.3390/genes13010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 02/04/2023] Open
Abstract
Osteogenesis imperfecta (OI) is an inherited disease of bone characterized by increased bone fragility. Here, we report the results of the molecular architecture of osteogenesis imperfecta research in patients from Bashkortostan Republic, Russia. In total, 16 mutations in COL1A1, 11 mutations in COL1A2, and 1 mutation in P3H1 and IFIMT5 genes were found in isolated states; 11 of them were not previously reported in literature. We found mutations in CLCN7, ALOX12B, PLEKHM1, ERCC4, ARSB, PTH1R, and TGFB1 that were not associated with OI pathogenesis in patients with increased bone fragility. Additionally, we found combined mutations (c.2869C>T, p. Gln957* in COL1A1 and c.1197+5G>A in COL1A2; c.579delT, p. Gly194fs in COL1A1 and c.1197+5G>A in COL1A2; c.2971G>C, p. Gly991Arg in COL1A2 and c.212G>C, p.Ser71Thr in FGF23; c.-14C>T in IFITM5 and c.1903C>T, p. Arg635* in LAMB3) in 4 patients with typical OI clinic phenotypes.
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Affiliation(s)
- Dina Nadyrshina
- Institute of Biochemistry and Genetics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.Z.); (I.M.); (R.K.)
- Departament of Genetics and Fundamental Medicine, Bashkir State University, 450076 Ufa, Russia
- Correspondence: ; Tel.:+7-9033559907
| | - Aliya Zaripova
- Institute of Biochemistry and Genetics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.Z.); (I.M.); (R.K.)
- Republican Medical Genetics Centre, 450076 Ufa, Russia
| | - Anton Tyurin
- Internal Medicine Department, Bashkir State Medical University, 450008 Ufa, Russia;
| | - Ildar Minniakhmetov
- Institute of Biochemistry and Genetics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.Z.); (I.M.); (R.K.)
- Republican Medical Genetics Centre, 450076 Ufa, Russia
- Internal Medicine Department, Bashkir State Medical University, 450008 Ufa, Russia;
| | | | - Rita Khusainova
- Institute of Biochemistry and Genetics—Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia; (A.Z.); (I.M.); (R.K.)
- Republican Medical Genetics Centre, 450076 Ufa, Russia
- Internal Medicine Department, Bashkir State Medical University, 450008 Ufa, Russia;
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16
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Fuji S, Tanaka K, Kishikawa S, Morita S, Doi M. Quartz crystal microbalance sensor for the detection of collagen model peptides based on the formation of triple helical structure. J Biosci Bioeng 2021; 133:168-173. [PMID: 34872873 DOI: 10.1016/j.jbiosc.2021.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 02/05/2023]
Abstract
Collagen is a major structural protein, and abnormalities in collagen structure can lead to several connective tissue diseases such as osteoporosis. We report the preparation of a collagen sensor using a synthetic peptide as proof of concept for detecting the collagen like peptides. The synthetic peptide 9-fluorenylmethyloxycarbonyl (Fmoc)-(prolyl-prolyl-glycine)7-OH was coupled to thiazolidine, which gets adsorbed on metal surfaces. Fmoc-(prolyl-prolyl-glycine)7-thiazolidine was immobilized on the surface of a quartz crystal microbalance (QCM) electrode used as a sensor probe. The collagen model peptide (prolyl-prolyl-glycine)10 could be detected, and the model peptide was directly adsorbed onto the surface of the electrode and was not removed by washing with hot water. Additionally, it was proved that the sensitivity of the probe could be enhanced to nanogram order by immobilizing the blocking reagent, Fmoc-prolyl-prolyl-glycine, within the gap of sensor probes on the electrode. The detectable mass of the model peptide decreased as the probe gap became narrower because of self-association of the probes. Moreover, the sensitivity of sensor probes also decreases as the gap between the probes becomes wider. Therefore, the optimum distance between the immobilized probes was determined from the simulation based on the experimental values. The association rate of the model peptide with sensor probes could be quantitatively determined when the distance between the probes was optimum, and this result suggested that most sensor probes could form a triple helical structure with the model peptide.
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Affiliation(s)
- Sota Fuji
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Noshima 77, Nada, Gobo, Wakayama 644-0023, Japan
| | - Kotaro Tanaka
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Noshima 77, Nada, Gobo, Wakayama 644-0023, Japan
| | - Shiho Kishikawa
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Noshima 77, Nada, Gobo, Wakayama 644-0023, Japan
| | - Seiichi Morita
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Noshima 77, Nada, Gobo, Wakayama 644-0023, Japan
| | - Masamitsu Doi
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Noshima 77, Nada, Gobo, Wakayama 644-0023, Japan.
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17
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ColGen: An end-to-end deep learning model to predict thermal stability of de novo collagen sequences. J Mech Behav Biomed Mater 2021; 125:104921. [PMID: 34758444 DOI: 10.1016/j.jmbbm.2021.104921] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/21/2021] [Indexed: 11/22/2022]
Abstract
Collagen is the most abundant structural protein in humans, with dozens of sequence variants accounting for over 30% of the protein in an animal body. The fibrillar and hierarchical arrangements of collagen are critical in providing mechanical properties with high strength and toughness. Due to this ubiquitous role in human tissues, collagen-based biomaterials are commonly used for tissue repairs and regeneration, requiring chemical and thermal stability over a range of temperatures during materials preparation ex vivo and subsequent utility in vivo. Collagen unfolds from a triple helix to a random coil structure during a temperature interval in which the midpoint or Tm is used as a measure to evaluate the thermal stability of the molecules. However, finding a robust framework to facilitate the design of a specific collagen sequence to yield a specific Tm remains a challenge, including using conventional molecular dynamics modeling. Here we propose a de novo framework to provide a model that outputs the Tm values of input collagen sequences by incorporating deep learning trained on a large data set of collagen sequences and corresponding Tm values. By using this framework, we are able to quickly evaluate how mutations and order in the primary sequence affect the stability of collagen triple helices. Specifically, we confirm that mutations to glycines, mutations in the middle of a sequence, and short sequence lengths cause the greatest drop in Tm values.
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18
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Ghatan S, Costantini A, Li R, De Bruin C, Appelman-Dijkstra NM, Winter EM, Oei L, Medina-Gomez C. The Polygenic and Monogenic Basis of Paediatric Fractures. Curr Osteoporos Rep 2021; 19:481-493. [PMID: 33945105 PMCID: PMC8551106 DOI: 10.1007/s11914-021-00680-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 01/19/2023]
Abstract
PURPOSE OF REVIEW Fractures are frequently encountered in paediatric practice. Although recurrent fractures in children usually unveil a monogenic syndrome, paediatric fracture risk could be shaped by the individual genetic background influencing the acquisition of bone mineral density, and therefore, the skeletal fragility as shown in adults. Here, we examine paediatric fractures from the perspective of monogenic and complex trait genetics. RECENT FINDINGS Large-scale genome-wide studies in children have identified ~44 genetic loci associated with fracture or bone traits whereas ~35 monogenic diseases characterized by paediatric fractures have been described. Genetic variation can predispose to paediatric fractures through monogenic risk variants with a large effect and polygenic risk involving many variants of small effects. Studying genetic factors influencing peak bone attainment might help in identifying individuals at higher risk of developing early-onset osteoporosis and discovering drug targets to be used as bone restorative pharmacotherapies to prevent, or even reverse, bone loss later in life.
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Affiliation(s)
- S Ghatan
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - A Costantini
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - R Li
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
| | - C De Bruin
- Department of Paediatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - N M Appelman-Dijkstra
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - E M Winter
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - L Oei
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carolina Medina-Gomez
- Translational Skeletal Genomics Group, Department of Internal Medicine, Erasmus MC University Medical Centre, Doctor Molewaterplein 40, Ee-571, 3015, GD, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus MC University Medical Centre, Rotterdam, The Netherlands.
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19
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Savige J, Storey H, Watson E, Hertz JM, Deltas C, Renieri A, Mari F, Hilbert P, Plevova P, Byers P, Cerkauskaite A, Gregory M, Cerkauskiene R, Ljubanovic DG, Becherucci F, Errichiello C, Massella L, Aiello V, Lennon R, Hopkinson L, Koziell A, Lungu A, Rothe HM, Hoefele J, Zacchia M, Martic TN, Gupta A, van Eerde A, Gear S, Landini S, Palazzo V, al-Rabadi L, Claes K, Corveleyn A, Van Hoof E, van Geel M, Williams M, Ashton E, Belge H, Ars E, Bierzynska A, Gangemi C, Lipska-Ziętkiewicz BS. Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria. Eur J Hum Genet 2021; 29:1186-1197. [PMID: 33854215 PMCID: PMC8384871 DOI: 10.1038/s41431-021-00858-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
The recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3-5). It identified 'mutational hotspots' (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that 'well-established' functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common 'incidental' findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3-COL4A5 genes remains a challenge.
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Affiliation(s)
- Judy Savige
- grid.1008.90000 0001 2179 088XDepartment of Medicine (MH and NH), The University of Melbourne, Parkville, VIC Australia
| | - Helen Storey
- grid.239826.40000 0004 0391 895XMolecular Genetics, Viapath Laboratories, Guy’s Hospital, London, UK
| | - Elizabeth Watson
- Elizabeth Watson, South West Genomic Laboratory Hub, North Bristol Trust, Bristol, UK
| | - Jens Michael Hertz
- grid.7143.10000 0004 0512 5013Jens Michael Hertz, Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Constantinos Deltas
- grid.6603.30000000121167908Center of Excellence in Biobanking and Biomedical Research and Molecule Medicine Center, University of Cyprus, Nicosia, Cyprus
| | - Alessandra Renieri
- grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pascale Hilbert
- Institute de Pathologie et de Genetique ASBL, Departement de Biologie Moleculaire, Gosselies, Belgium
| | - Pavlina Plevova
- grid.412727.50000 0004 0609 0692Department of Medical Genetics, and Department of Biomedical Sciences, University Hospital of Ostrava, Ostrava, Czech Republic
| | - Peter Byers
- grid.34477.330000000122986657Departments of Pathology and Medicine (Medical Genetics), University of Washington, Seattle, WA USA
| | - Agne Cerkauskaite
- grid.6441.70000 0001 2243 2806Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Martin Gregory
- grid.223827.e0000 0001 2193 0096Division of Nephrology, Department of Medicine, University of Utah Health, Salt Lake City, UT USA
| | - Rimante Cerkauskiene
- grid.6441.70000 0001 2243 2806Clinic of Pediatrics, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Danica Galesic Ljubanovic
- grid.412095.b0000 0004 0631 385XDepartment of Pathology, University of Zagreb, School of Medicine, Dubrava University Hospital, Zagreb, Croatia
| | - Francesca Becherucci
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Carmela Errichiello
- grid.411477.00000 0004 1759 0844Nephrology Unit and Meyer Children’s University Hospital, Firenze, Italy
| | - Laura Massella
- grid.414125.70000 0001 0727 6809Division of Nephrology and Dialysis, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Valeria Aiello
- grid.6292.f0000 0004 1757 1758Department of Experimental Diagnostic and Specialty Medicine (DIMES), Nephrology, Dialysis and Renal Transplant Unit, S. Orsola Hospital, University of Bologna, Bologna, Italy
| | - Rachel Lennon
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Louise Hopkinson
- grid.5379.80000000121662407Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ania Koziell
- grid.13097.3c0000 0001 2322 6764School of Immunology and Microbial Sciences, Faculty of Life Sciences, King’s College London, London, UK
| | - Adrian Lungu
- grid.415180.90000 0004 0540 9980Fundeni Clinical Institute, Pediatric Nephrology Department, Bucharest, Romania
| | | | - Julia Hoefele
- grid.6936.a0000000123222966Institute of Human Genetics, Technical University of Munich, München, Germany
| | | | - Tamara Nikuseva Martic
- grid.4808.40000 0001 0657 4636Department of Biology, School of Medicine University of Zagreb, Zagreb, Croatia
| | - Asheeta Gupta
- grid.415246.00000 0004 0399 7272Birmingham Children’s Hospital, Birmingham, UK
| | - Albertien van Eerde
- grid.5477.10000000120346234Departments of Genetics and Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuela Landini
- grid.8404.80000 0004 1757 2304Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Viviana Palazzo
- grid.411477.00000 0004 1759 0844Medical Genetics Unit, Meyer Children’s University Hospital, Florence, Italy
| | - Laith al-Rabadi
- grid.223827.e0000 0001 2193 0096Health Sciences Centre, University of UTAH, Salt Lake City, UT USA
| | - Kathleen Claes
- grid.410569.f0000 0004 0626 3338Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Evelien Van Hoof
- grid.410569.f0000 0004 0626 3338Center for Human Genetics, University Hospitals and KU Leuven, Leuven, Belgium
| | - Micheel van Geel
- grid.412966.e0000 0004 0480 1382Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maggie Williams
- grid.416201.00000 0004 0417 1173Bristol Genetics Laboratory Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Emma Ashton
- grid.420468.cNorth East Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Hendica Belge
- grid.10417.330000 0004 0444 9382Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elisabeth Ars
- grid.7080.f0000 0001 2296 0625Inherited Kidney Disorders, Fundacio Puigvert, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Agnieszka Bierzynska
- grid.5337.20000 0004 1936 7603Bristol Renal Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Concetta Gangemi
- grid.411475.20000 0004 1756 948XDivision of Nephrology and Dialysis, University Hospital of Verona, Verona, Italy
| | - Beata S. Lipska-Ziętkiewicz
- grid.11451.300000 0001 0531 3426Centre for Rare Diseases, and Clinical Genetics Unit, Medical University of Gdansk, Gdansk, Poland
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20
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Hartmann J, Zacharias M. Mechanism of collagen folding propagation studied by Molecular Dynamics simulations. PLoS Comput Biol 2021; 17:e1009079. [PMID: 34101748 PMCID: PMC8224937 DOI: 10.1371/journal.pcbi.1009079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/24/2021] [Accepted: 05/13/2021] [Indexed: 11/19/2022] Open
Abstract
Collagen forms a characteristic triple helical structure and plays a central role for stabilizing the extra-cellular matrix. After a C-terminal nucleus formation folding proceeds to form long triple-helical fibers. The molecular details of triple helix folding process is of central importance for an understanding of several human diseases associated with misfolded or unstable collagen fibrils. However, the folding propagation is too rapid to be studied by experimental high resolution techniques. We employed multiple Molecular Dynamics simulations starting from unfolded peptides with an already formed nucleus to successfully follow the folding propagation in atomic detail. The triple helix folding was found to propagate involving first two chains forming a short transient template. Secondly, three residues of the third chain fold on this template with an overall mean propagation of ~75 ns per unit. The formation of loops with multiples of the repeating unit was found as a characteristic misfolding event especially when starting from an unstable nucleus. Central Gly→Ala or Gly→Thr substitutions resulted in reduced stability and folding rates due to structural deformations interfering with folding propagation. The extracellular matrix is stabilized by collagen, a fibrillar protein structure, which represents the most abundant protein of the human body. Collagen consists of three peptide chains that form an elongated triple helix with a repeating and largely conserved sequence pattern of two proline (or hydroxyproline) residues followed by a glycine. Several human diseases are associated with mutations in collagen. The folding propagation is the most critical step in the collagen structure formation and not well understood. We have used multiple Molecular Dynamics simulations to specifically investigate the mechanism of triple helix propagation and how it is affected by mutations. The folding propagation was found to involve first two chains forming a short transient template followed by three residues of the third chain to fold on this template. Additional simulations were used to characterize misfolding events such as loop formation and the effect of glycine substitutions on collagen folding.
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Affiliation(s)
- Julian Hartmann
- Center for Functional Protein Assemblies, Technische Universität München, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technische Universität München, Garching, Germany
- * E-mail:
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21
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Bellaye PS, Burgy O, Bonniaud P, Kolb M. HSP47: a potential target for fibrotic diseases and implications for therapy. Expert Opin Ther Targets 2021; 25:49-62. [PMID: 33287600 DOI: 10.1080/14728222.2021.1861249] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Introduction: Chronic fibrotic disorders are challenging clinical problems. The major challenge is the identification of specific targets expressed selectively in fibrotic tissues. Collagen accumulation is the hallmark fibrosis. HSP47 is a collagen-specific chaperon with critical role in collagen folding. This review discusses the anti-fibrotic potential of HSP47. Areas covered: This review compiles data retrieved from the PubMed database with keywords 'HSP47+fibrosis' from 01/2005 to 06/2020. We examined 1) collagen biology and its role in fibrotic diseases, 2) HSP47 role in fibrosis, 3) HSP47 inhibition strategies and 4) clinical investigations. The identification of the HSP47-collagen binding site led to the development of methods to screen HSP47 inhibitors with anti-fibrotic potential. Specific in vivo delivery systems of HSP47 siRNA to fibrotic tissue reduced collagen production/secretion associated with fibrosis inhibition in preclinical models. This strategy is about to be tested in clinical trials. Expert opinion: As a collagen-specific chaperon, HSP47 is a promising therapeutic target in fibrosis. Preclinical models have shown encouraging anti-fibrotic results. Anti-HSP47 strategies need to be further evaluated in clinical trials. The increase in circulating-HSP47 in lung fibrosis patients highlights the potential of HSP47 as a noninvasive biomarker and may represent an important step toward personalized medicine in fibrotic disorders.
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Affiliation(s)
- Pierre-Simon Bellaye
- Centre George-Franrçois Leclerc, Nuclear Medicine department, Plateforme d'imagerie et de radiothérapie préclinique, 1 rue du professeur Marion, Dijon, France.,Centre de Référence Constitutif des Maladies Pulmonaires Rares de l'Adultes de Dijon, Réseau OrphaLung, Filère RespiFil, Centre Hospitalier Universitaire de Bourgogne , Dijon,France
| | - Olivier Burgy
- Centre de Référence Constitutif des Maladies Pulmonaires Rares de l'Adultes de Dijon, Réseau OrphaLung, Filère RespiFil, Centre Hospitalier Universitaire de Bourgogne , Dijon,France.,INSERM U1231 Department HSP-pathies 7 Boulevard Jeanne d'Arc ,Dijon France
| | - Philippe Bonniaud
- Centre de Référence Constitutif des Maladies Pulmonaires Rares de l'Adultes de Dijon, Réseau OrphaLung, Filère RespiFil, Centre Hospitalier Universitaire de Bourgogne , Dijon,France
| | - Martin Kolb
- McMaster University, Department of medicine, FIRH, 50 Charlton Avenue East, Hamilton , Ontario, Canada
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22
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Pragnère S, Auregan JC, Bosser C, Linglart A, Bensidhoum M, Hoc T, Nouguier-Lehon C, Chaussain C. Human dentin characteristics of patients with osteogenesis imperfecta: insights into collagen-based biomaterials. Acta Biomater 2021; 119:259-267. [PMID: 33122145 DOI: 10.1016/j.actbio.2020.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 11/28/2022]
Abstract
Osteogenesis imperfecta (OI), also known as "brittle bone disease", is a rare genetic disorder of the skeleton, whose most benign form I corresponds to autosomal dominant mutations in the genes encoding type I collagen (COLA1, COLA2). Several associated skeletal manifestations are often observed but, surprisingly, while dentin defects often reflect genetic bone disorders, about half of OI patients have no obvious oral manifestations. Here, we investigated the collagen, mineral and mechanical properties of dentin from deciduous teeth collected from patients with mild form of OI and displaying no obvious clinical signs of dentinogenesis imperfecta. For the first time, an increase in the hardness of OI dentin associated with an increase in mineral content compared to healthy patients was reported. In addition, OI altered the tissue characteristics of the dentin-enamel junction but the interfacial gradient was preserved. The impact of changes in molecular structure due to mutations in OI was assessed by Raman microspectroscopy. Our results highlighted a change in the hydroxyproline-proline ratio in direct association with collagen mineralization. Our findings suggest that the evaluation of teeth could be an important aid for mild types of OI that are often difficult to diagnose clinically and provide experimental evidence that hydroxyproline content should be considered in future studies on collagen-based biomaterials.
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Affiliation(s)
- S Pragnère
- Equipex IVTV, Centrale Innovation, 64 Chemin des Mouilles, 69130 Ecully, France
| | - J-C Auregan
- Université de Paris, B3OA, UMR CNRS 7052, INSERM U1271, 10 Avenue de Verdun, 75010 Paris, France; AP-HP, Antoine Béclère Université Paris-Saclay hospital, Orthopeadics Department, 157, rue de la Porte de Trivaux, 92140 Clamart, France
| | - C Bosser
- Equipex IVTV, Centrale Innovation, 64 Chemin des Mouilles, 69130 Ecully, France
| | - A Linglart
- Université de Paris Saclay, Le Kremlin-Bicêtre, France; AP-HP, Department of Endocrinology and Diabetology for children, Reference Center for Rare Disorders of the Calcium and Phosphate Metabolism, Filière OSCAR and Platform of expertise for rare diseases Paris-Sud, Bicêtre Paris-Saclay Hospital, Le Kremlin-Bicêtre, France
| | - M Bensidhoum
- Université de Paris, B3OA, UMR CNRS 7052, INSERM U1271, 10 Avenue de Verdun, 75010 Paris, France
| | - T Hoc
- Université de Paris, B3OA, UMR CNRS 7052, INSERM U1271, 10 Avenue de Verdun, 75010 Paris, France; Mechanical Department, MSGMGC, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully Cedex, France.
| | - C Nouguier-Lehon
- Université de Lyon, LTDS UMR CNRS 5513, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully Cedex, France
| | - C Chaussain
- Université de Paris, Dental School, UR2496, Montrouge, F-92120, France; AP-HP Reference Center for Rare Disorders of the Calcium and Phosphate Metabolism (OSCAR, ERN Bond), Dental Medicine Department, Bretonneau Hospital, GHN, 75018 Paris, France
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23
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Wei W, Li D, Cai X, Liu Z, Bai Z, Xiao J. Peptide Probes with Aromatic Residues Tyr and Phe at the X Position Show High Specificity for Targeting Denatured Collagen in Tissues. ACS OMEGA 2020; 5:33075-33082. [PMID: 33403269 PMCID: PMC7774067 DOI: 10.1021/acsomega.0c04684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The construction of potent peptide probes for selectively detecting denatured collagen is crucial for a variety of widespread diseases. However, all of the denatured collagen-targeting peptide probes found till date primarily utilized the repetitive (Gly-X-Y) n sequences with exclusively imino acids Pro and Hyp in the X and Y positions, which stabilized the triple helical conformation of the peptide probes, resulting in severe obstacles for their clinical applications. A novel series of peptide probes have been constructed by incorporating nonimino acids at the X position of the (GPO)3GXO(GPO)4 sequence, while the X-site residue is varied as Tyr, Phe, Asp, and Ala, respectively. Peptide probes FAM-GYO and FAM-GFO containing aromatic residues Tyr and Phe at the X position showed similarly high binding affinity and tissue-staining efficacy as the well-established peptide probe FAM-GPO, while peptide probes FAM-GDO and FAM-GAO with the corresponding charged residue Asp and the hydrophobic residue Ala indicated much weaker binding affinity and tissue-staining capability. Furthermore, FAM-GYO and FAM-GFO could specifically detect denatured collagen in different types of mouse connective tissues and efficiently stain various human pathological tissues. We have revealed for the first time that the incorporation of nonimino acids, particularly aromatic residues at the X and Y positions of the repetitive (Gly-X-Y) n sequences, may provide a convenient strategy to create novel robust collagen-targeting peptide probes, which have promising diagnostic applications in collagen-involved diseases.
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Affiliation(s)
- Wenyu Wei
- 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
| | - Dongfang 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
| | - Xiangdong Cai
- 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
| | - Zhao 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
| | - Zhongtian Bai
- The Second Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, 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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24
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Shi J, Ren M, Jia J, Tang M, Guo Y, Ni X, Shi T. Corrigendum: Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease. Front Pharmacol 2020; 10:1603. [PMID: 32116662 PMCID: PMC7013177 DOI: 10.3389/fphar.2019.01603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fphar.2019.01200.].
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Affiliation(s)
- Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Meng Ren
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Muxue Tang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
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25
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Yao L, Liu Z, Yu J, Luo L, Wang J, Xiao J. Morphology of Osteogenesis Imperfecta Collagen Mimetic Peptide Assemblies Correlates with the Identity of Glycine-Substituting Residue. Chembiochem 2019; 20:3013-3019. [PMID: 31237990 DOI: 10.1002/cbic.201900114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/02/2019] [Indexed: 11/07/2022]
Abstract
Osteogenesis imperfecta (OI) is a hereditary bone disorder with various phenotypes ranging from mild multiple fractures to perinatal lethal cases, and it mainly results from the substitution of Gly by a bulkier residue in type I collagen. Triple-helical peptide models of Gly mutations have been widely utilized to decipher the etiology of OI, although these studies are mainly limited to characterizing the peptide features, such as stability and conformation in the solution state. Herein, we have constructed a new series of triple-helical peptides DD(GPO)5 ZPO(GPO)4 DD (Z=Ala, Arg, Asp, Cys, Glu, Ser, and Val) mimicking the most common types of observed OI cases. The inclusion of special terminal aspartic acids enables these collagen mimetic peptides to self-assemble to form nanomaterials upon the trigger of lanthanide ions. We have for the first time systematically evaluated the effect of different OI mutations on the aggregated state of collagen mimetic peptides. We have revealed that the identity of the Gly-substituting residue plays a determinant role in the morphology and secondary structure of the collagen peptide assemblies, showing that bulkier residues tend to result in a disruptive secondary structure and defective morphology, which lead to more severe OI phenotypes. These findings of osteogenesis imperfecta collagen mimetic peptides in the aggregation state provide novel perspectives on the molecular mechanism of osteogenesis imperfecta, and may aid the development of new therapeutic strategies.
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Affiliation(s)
- Linyan Yao
- 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
| | - Zhao 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
| | - Jingyuan Yu
- 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
| | - Liting Luo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and, Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Jie Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and, Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, 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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26
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Shi J, Ren M, Jia J, Tang M, Guo Y, Ni X, Shi T. Genotype-Phenotype Association Analysis Reveals New Pathogenic Factors for Osteogenesis Imperfecta Disease. Front Pharmacol 2019; 10:1200. [PMID: 31680973 PMCID: PMC6803541 DOI: 10.3389/fphar.2019.01200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
Osteogenesis imperfecta (OI), mainly caused by structural abnormalities of type I collagen, is a hereditary rare disease characterized by increased bone fragility and reduced bone mass. Clinical manifestations of OI mostly include multiple repeated bone fractures, thin skin, blue sclera, hearing loss, cardiovascular and pulmonary system abnormalities, triangular face, dentinogenesis imperfecta (DI), and walking with assistance. Currently, 20 causative genes with 18 subtypes have been identified for OI, of them, variations in COL1A1 and COL1A2 have been demonstrated to be major causative factors to OI. However, the complexity of the bone formation process indicates that there are potential new pathogenic genes associated with OI. To comprehensively explore the underlying mechanism of OI, we conducted association analysis between genotypes and phenotypes of OI diseases and found that mutations in COL1A1 and COL1A2 contributed to a large proportion of the disease phenotypes. We categorized the clinical phenotypes and the genotypes based on the variation types for those 155 OI patients collected from literature, and association study revealed that three phenotypes (bone deformity, DI, walking with assistance) were enriched in two variation types (the Gly-substitution missense and groups of frameshift, nonsense, and splicing variations). We also identified four novel variations (c.G3290A (p.G1097D), c.G3289C (p.G1097R), c.G3289A (p.G1097S), c.G3281A (p.G1094D)) in gene COL1A1 and two novel variations (c.G2332T (p.G778C), c.G2341T (p.G781C)) in gene COL1A2, which could potentially contribute to the disease. In addition, we identified several new potential pathogenic genes (ADAMTS2, COL5A2, COL8A1) based on the integration of protein–protein interaction and pathway enrichment analysis. Our study provides new insights into the association between genotypes and phenotypes of OI and novel information for dissecting the underlying mechanism of the disease.
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Affiliation(s)
- Jingru Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Meng Ren
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jinmeng Jia
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Muxue Tang
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xin Ni
- Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatrics, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.,Big Data and Engineering Research Center, Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
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27
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Hoop CL, Kemraj AP, Wang B, Gahlawat S, Godesky M, Zhu J, Warren HR, Case DA, Shreiber DI, Baum J. Molecular underpinnings of integrin binding to collagen-mimetic peptides containing vascular Ehlers-Danlos syndrome-associated substitutions. J Biol Chem 2019; 294:14442-14453. [PMID: 31406019 DOI: 10.1074/jbc.ra119.009685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Indexed: 11/06/2022] Open
Abstract
Collagens carry out critical extracellular matrix (ECM) functions by interacting with numerous cell receptors and ECM components. Single glycine substitutions in collagen III, which predominates in vascular walls, result in vascular Ehlers-Danlos syndrome (vEDS), leading to arterial, uterine, and intestinal rupture and an average life expectancy of <50 years. Collagen interactions with integrin α2β1 are vital for platelet adhesion and activation; however, how these interactions are impacted by vEDS-associated mutations and by specific amino acid substitutions is unclear. Here, we designed collagen-mimetic peptides (CMPs) with previously reported Gly → Xaa (Xaa = Ala, Arg, or Val) vEDS substitutions within a high-affinity integrin α2β1-binding motif, GROGER. We used these peptides to investigate, at atomic-level resolution, how these amino acid substitutions affect the collagen III-integrin α2β1 interaction. Using a multitiered approach combining biological adhesion assays, CD, NMR, and molecular dynamics (MD) simulations, we found that these substitutions differentially impede human mesenchymal stem cell spreading and integrin α2-inserted (α2I) domain binding to the CMPs and were associated with triple-helix destabilization. Although an Ala substitution locally destabilized hydrogen bonding and enhanced mobility, it did not significantly reduce the CMP-integrin interactions. MD simulations suggested that bulkier Gly → Xaa substitutions differentially disrupt the CMP-α2I interaction. The Gly → Arg substitution destabilized CMP-α2I side-chain interactions, and the Gly → Val change broke the essential Mg2+ coordination. The relationship between the loss of functional binding and the type of vEDS substitution provides a foundation for developing potential therapies for managing collagen disorders.
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Affiliation(s)
- Cody L Hoop
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Allysa P Kemraj
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Baifan Wang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Sonal Gahlawat
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Madison Godesky
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jie Zhu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Haley R Warren
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - David I Shreiber
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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28
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Takeda N, Komuro I. Genetic basis of hereditary thoracic aortic aneurysms and dissections. J Cardiol 2019; 74:136-143. [DOI: 10.1016/j.jjcc.2019.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
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29
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Lu Y, Zhang S, Wang Y, Ren X, Han J. Molecular mechanisms and clinical manifestations of rare genetic disorders associated with type I collagen. Intractable Rare Dis Res 2019; 8:98-107. [PMID: 31218159 PMCID: PMC6557237 DOI: 10.5582/irdr.2019.01064] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Type I collagen is an important structural protein of bone, skin, tendon, ligament and other connective tissues. It is initially synthesized as a precursor form, procollagen, consisting of two identical pro-α1(I) and one proα2(I) chains, encoded by COL1A1 and COL1A2, respectively. The N- and C- terminal propeptides of procollagen are cleavage by N-proteinase and C-proteinase correspondingly, to form the central triple helix structure with Gly-X-Y repeat units. Mutations of COL1A1 and COL1A2 genes are associated with osteogenesis imperfecta, some types of Ehlers-Danlos syndrome, Caffey diseases, and osteogenesis imperfect/Ehlers- Danlos syndrome overlapping diseases. Clinical symptoms caused by different variations can be variable or similar, mild to lethal, and vice versa. We reviewed the relationship between clinical manifestations and type I collagen - related rare genetic disorders and their possible molecular mechanisms for different mutations and disorders.
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Affiliation(s)
- Yanqin Lu
- Key Laboratory for Biotech-Drugs of National Health Commission, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Ji'nan, China
- Address correspondence to:Dr. Yanqin Lu, Shandong First Medical University & Shandong Academy of Medical Sciences, 18877 Jingshi Road, Ji'nan 250062, China. E-mail:
| | - Shie Zhang
- Key Laboratory for Biotech-Drugs of National Health Commission, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Ji'nan, China
| | - Yanzhou Wang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Ji'nan, China
| | - Xiuzhi Ren
- Department of Orthopaedic Surgery, The People’s Hospital of Wuqing District, Tianjin, China
| | - Jinxiang Han
- Key Laboratory for Biotech-Drugs of National Health Commission, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Ji'nan, China
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30
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Sun X, Liu Z, Zhao S, Xu X, Wang S, Guo C, Xiao J. A self-assembling collagen mimetic peptide system to simultaneously characterize the effects of osteogenesis imperfecta mutations on conformation, assembly and activity. J Mater Chem B 2019. [DOI: 10.1039/c9tb00086k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have created a self-assembling collagen mimetic peptide system which for the first time facilitates simultaneous characterization of the effects of osteogenesis imperfecta mutations on stability, conformation, assembly and activity.
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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
| | - Zhao 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
| | - Sha Zhao
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
- Beijing NMR Centre
| | - Xiaojun Xu
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
- Beijing NMR Centre
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
- Beijing NMR Centre
| | - Chengchen Guo
- Department of Biomedical Engineering
- Tufts University
- Medford
- USA
| | - 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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31
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Tokmina-Roszyk M, Fields GB. Dissecting MMP P 10' and P 11' subsite sequence preferences, utilizing a positional scanning, combinatorial triple-helical peptide library. J Biol Chem 2018; 293:16661-16676. [PMID: 30185620 DOI: 10.1074/jbc.ra118.003266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that remodel the extracellular matrix environment and mitigate outside-in signaling. Loss of regulation of MMP activity plays a role in numerous pathological states. In particular, aberrant collagenolysis affects tumor invasion and metastasis, osteoarthritis, and cardiovascular and neurodegenerative diseases. To evaluate the collagen sequence preferences of MMPs, a positional scanning synthetic combinatorial library was synthesized herein and was used to investigate the P10' and P11' substrate subsites. The scaffold for the library was a triple-helical peptide mimic of the MMP cleavage site in types I-III collagen. A FRET-based enzyme activity assay was used to evaluate the sequence preferences of eight MMPs. Deconvolution of the library data revealed distinct motifs for several MMPs and discrimination among closely related MMPs. On the basis of the screening results, several individual peptides were designed and evaluated. A triple-helical substrate incorporating Asp-Lys in the P10'-P11' subsites offered selectivity between MMP-14 and MMP-15, whereas Asp-Lys or Trp-Lys in these subsites discriminated between MMP-2 and MMP-9. Future screening of additional subsite positions will enable the design of selective triple-helical MMP probes that could be used for monitoring in vivo enzyme activity and enzyme-facilitated drug delivery. Furthermore, selective substrates could serve as the basis for the design of specific triple-helical peptide inhibitors targeting only those MMPs that play a detrimental role in a disease of interest.
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Affiliation(s)
- Michal Tokmina-Roszyk
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and
| | - Gregg B Fields
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and .,the Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
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32
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Makareeva E, Sun G, Mirigian LS, Mertz EL, Vera JC, Espinoza NA, Yang K, Chen D, Klein TE, Byers PH, Leikin S. Substitutions for arginine at position 780 in triple helical domain of the α1(I) chain alter folding of the type I procollagen molecule and cause osteogenesis imperfecta. PLoS One 2018; 13:e0200264. [PMID: 29990383 PMCID: PMC6039012 DOI: 10.1371/journal.pone.0200264] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/24/2018] [Indexed: 01/30/2023] Open
Abstract
OI is a clinically and genetically heterogeneous disorder characterized by bone fragility. More than 90% of patients are heterozygous for mutations in type I collagen genes, COL1A1 and COL1A2, and a common mutation is substitution for an obligatory glycine in the triple helical Gly-X-Y repeats. Few non-glycine substitutions in the triple helical domain have been reported; most result in Y-position substitutions of arginine by cysteine. Here, we investigated leucine and cysteine substitutions for one Y-position arginine, p.Arg958 (Arg780 in the triple helical domain) of proα1(I) chains that cause mild OI. We compared their effects with two substitutions for glycine located in close proximity. Like substitutions for glycine, those for arginine reduced the denaturation temperature of the whole molecule and caused asymmetric posttranslational overmodification of the chains. Circular dichroism and increased susceptibility to cleavage by MMP1, MMP2 and catalytic domain of MMP1 revealed significant destabilization of the triple helix near the collagenase cleavage site. On a cellular level, we observed slower triple helix folding and intracellular collagen retention, which disturbed the Endoplasmic Reticulum function and affected matrix deposition. Molecular dynamic modeling suggested that Arg780 substitutions disrupt the triple helix structure and folding by eliminating hydrogen bonds of arginine side chains, in addition to preventing HSP47 binding. The pathogenic effects of these non-glycine substitutions in bone are probably caused mostly by procollagen misfolding and its downstream effects.
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Affiliation(s)
- Elena Makareeva
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guoli Sun
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lynn S. Mirigian
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward L. Mertz
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Juan C. Vera
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nydea A. Espinoza
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathleen Yang
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Diana Chen
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Teri E. Klein
- Department of Genetics, Stanford University, Palo Alto, California, United States of America
| | - Peter H. Byers
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America
| | - Sergey Leikin
- Section on Physical Biochemistry, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Mekkat A, Poppleton E, An B, Visse R, Nagase H, Kaplan DL, Brodsky B, Lin YS. Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage. J Struct Biol 2018; 203:247-254. [PMID: 29763735 DOI: 10.1016/j.jsb.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 11/18/2022]
Abstract
Cleavage of collagen by collagenases such as matrix metalloproteinase 1 (MMP-1) is a key step in development, tissue remodeling, and tumor proliferation. The abundant heterotrimeric type I collagen composed of two α1(I) chains and one α2(I) chain is efficiently cleaved by MMP-1 at a unique site in the triple helix, a process which may be initiated by local unfolding within the peptide chains. Atypical homotrimers of the α1(I) chain, found in embryonic and cancer tissues, are very resistant to MMP cleavage. To investigate MMP-1 cleavage, recombinant homotrimers were constructed with sequences from the MMP cleavage regions of human collagen chains inserted into a host bacterial collagen protein system. All triple-helical constructs were cleaved by MMP-1, with α2(I) homotrimers cleaved efficiently at a rate similar to that seen for α1(II) and α1(III) homotrimers, while α1(I) homotrimers were cleaved at a much slower rate. The introduction of destabilizing Gly to Ser mutations within the human collagenase susceptible region of the α2(I) chain did not interfere with MMP-1 cleavage. Molecular dynamics simulations indicated a greater degree of transient hydrogen bond breaking in α2(I) homotrimers compared with α1(I) homotrimers at the MMP-1 cleavage site, and showed an extensive disruption of hydrogen bonding in the presence of a Gly to Ser mutation, consistent with chymotrypsin digestion results. This study indicates that α2(I) homotrimers are susceptible to MMP-1, proves that the presence of an α1(I) chain is not a requirement for α2(I) cleavage, and supports the importance of local unfolding of α2(I) in collagenase cleavage.
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Affiliation(s)
- Arya Mekkat
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Erik Poppleton
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Bo An
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Robert Visse
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Hideaki Nagase
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Barbara Brodsky
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, USA.
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Qiu Y, Mekkat A, Yu H, Yigit S, Hamaia S, Farndale RW, Kaplan DL, Lin YS, Brodsky B. Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding. J Struct Biol 2018; 203:255-262. [PMID: 29758270 DOI: 10.1016/j.jsb.2018.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 01/31/2023]
Abstract
Gly missense mutations in type I collagen, which replace a conserved Gly in the repeating (Gly-Xaa-Yaa)n sequence with a larger residue, are known to cause Osteogenesis Imperfecta (OI). The clinical consequences of such mutations range from mild to lethal, with more serious clinical severity associated with larger Gly replacement residues. Here, we investigate the influence of the identity of the residue replacing Gly within and adjacent to the integrin binding 502GFPGER507 sequence on triple-helix structure, stability and integrin binding using a recombinant bacterial collagen system. Recombinant collagens were constructed with Gly substituted by Ala, Ser or Val at four positions within the integrin binding region. All constructs formed a stable triple-helix structure with a small decrease in melting temperature. Trypsin was used to probe local disruption of the triple helix, and Gly to Val replacements made the triple helix trypsin sensitive at three of the four sites. Any mutation at Gly505, eliminated integrin binding, while decreased integrin binding affinity was observed in the replacement of Gly residues at Gly502 following the order Val > Ser > Ala. Molecular dynamics simulations indicated that all Gly replacements led to transient disruption of triple-helix interchain hydrogen bonds in the region of the Gly replacement. These computational and experimental results lend insight into the complex molecular basis of the varying clinical severity of OI.
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Affiliation(s)
- Yimin Qiu
- Department of Biomedical Engineering, Tufts University, United States
| | - Arya Mekkat
- Department of Chemistry, Tufts University, United States
| | - Hongtao Yu
- Department of Biomedical Engineering, Tufts University, United States; Department of Chemistry, Tufts University, United States
| | - Sezin Yigit
- Department of Biomedical Engineering, Tufts University, United States
| | - Samir Hamaia
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, United States
| | - Barbara Brodsky
- Department of Biomedical Engineering, Tufts University, United States.
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Collet C, Ostertag A, Ricquebourg M, Delecourt M, Tueur G, Isidor B, Guillot P, Schaefer E, Javier RM, Funck-Brentano T, Orcel P, Laplanche JL, Cohen-Solal M. Primary Osteoporosis in Young Adults: Genetic Basis and Identification of Novel Variants in Causal Genes. JBMR Plus 2017; 2:12-21. [PMID: 30283887 PMCID: PMC6124172 DOI: 10.1002/jbm4.10020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 02/01/2023] Open
Abstract
Genetic determinants contribute to osteoporosis and enhance the risk of fracture. Genomewide association studies of unselected population-based individuals or families have identified polymorphisms in several genes related to low bone density, but not in osteoporotic patients with Z-score < -2.0 SD with fragility fracture(s). The aim of this study was to determine the causal genes of idiopathic osteoporosis in the adulthood. Also, we used next-generation sequencing of candidate genes in a cohort of 123 young or middle-aged adults with idiopathic osteoporosis. All patients were included if they had a low bone mineral density (Z-score < -2 SD), a diagnosis before age 55 years (mean ± SD, 48.4 ± 10.6 years; mean ± SD age at first fracture, 30.4 ± 17.4 years) and fracture or not. We found that 11 patients carried rare or novel variants in COL1A2 (n = 4), PLS3 (n = 2), WNT1 (n = 4), or DKK1 (n = 1). We showed a high prevalence of pathogenic variants in LRP5: 22 patients (17.8%) had the p.Val667Met variant, including three at the homozygous level and 16 (13%) carrying a novel or very rare variant. Functional analysis revealed that the LRP5 missense variants resulted in reduced luciferase activity, which indicates reduced activation of canonical WNT signaling. The clinical phenotype of patients carrying causal gene variants was indistinguishable. In conclusion, molecular screening of young osteoporotic adults revealed several variants and could be useful to characterize susceptibility genes for personalizing treatment, in particular for the new anabolic drugs.© 2017 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
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Affiliation(s)
- Corinne Collet
- Department of Biochemistry and Genetics Hospital Lariboisiere Paris France.,INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
| | - Agnès Ostertag
- INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
| | - Manon Ricquebourg
- INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
| | - Marine Delecourt
- Department of Biochemistry and Genetics Hospital Lariboisiere Paris France
| | - Giulia Tueur
- Department of Biochemistry and Genetics Hospital Lariboisiere Paris France
| | - Bertrand Isidor
- Genetic Medical Department Centre Hospitalier Universitaire (CHU) de Nantes Nantes France
| | - Pascale Guillot
- Genetic Medical Department Centre Hospitalier Universitaire (CHU) de Nantes Nantes France
| | - Elise Schaefer
- Genetic Medical Department les Hopitaux Universitaires de Strasbourg Strasbourg France
| | - Rose-Marie Javier
- Rheumatology Department les Hopitaux Universitaires de Strasbourg Strasbourg France
| | - Thomas Funck-Brentano
- INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
| | - Philippe Orcel
- INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
| | | | - Martine Cohen-Solal
- INSERM U1132 University Paris-Diderot Paris France.,Department of Rheumatology Hospital Lariboisiere Paris France
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Amar S, Smith L, Fields GB. Matrix metalloproteinase collagenolysis in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2017; 1864:1940-1951. [PMID: 28456643 PMCID: PMC5605394 DOI: 10.1016/j.bbamcr.2017.04.015] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 01/08/2023]
Abstract
The proteolytic processing of collagen (collagenolysis) is critical in development and homeostasis, but also contributes to numerous pathologies. Mammalian interstitial collagenolytic enzymes include members of the matrix metalloproteinase (MMP) family and cathepsin K. While MMPs have long been recognized for their ability to catalyze the hydrolysis of collagen, the roles of individual MMPs in physiological and pathological collagenolysis are less defined. The use of knockout and mutant animal models, which reflect human diseases, has revealed distinct collagenolytic roles for MT1-MMP and MMP-13. A better understanding of temporal and spatial collagen processing, along with the knowledge of the specific MMP involved, will ultimately lead to more effective treatments for cancer, arthritis, cardiovascular conditions, and infectious diseases. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Sabrina Amar
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA.
| | - Lyndsay Smith
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA.
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL 33458, USA.
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Cheng X, Shao Z, Li C, Yu L, Raja MA, Liu C. Isolation, Characterization and Evaluation of Collagen from Jellyfish Rhopilema esculentum Kishinouye for Use in Hemostatic Applications. PLoS One 2017; 12:e0169731. [PMID: 28103327 PMCID: PMC5245839 DOI: 10.1371/journal.pone.0169731] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022] Open
Abstract
Hemostat has been a crucial focus since human body is unable to control massive blood loss, and collagen proves to be an effective hemostat in previous studies. In this study, collagen was isolated from the mesoglea of jellyfish Rhopilema esculentum Kishinouye and its hemostatic property was studied. The yields of acid-soluble collagen (ASC) and pepsin-soluble (PSC) were 0.12% and 0.28% respectively. The SDS-PAGE patterns indicated that the collagen extracted from jellyfish mesoglea was type I collagen. The lyophilized jellyfish collagen sponges were cross-linked with EDC and interconnected networks in the sponges were revealed by scanning electron microscope (SEM). Collagen sponges exhibited higher water absorption rates than medical gauze and EDC/NHS cross-linking method could improve the stability of the collagen sponges. Compared with medical gauze groups, the blood clotting indexes (BCIs) of collagen sponges were significantly decreased (P < 0.05) and the concentration of collagen also had an influence on the hemostatic property (P < 0.05). Collagen sponges had an improved hemostatic ability compared to the gauze control in tail amputation rat models. Hemostatic mechanism studies showed that hemocytes and platelets could adhere and aggregate on the surface of collagen sponge. All properties make jellyfish collagen sponge to be a suitable candidate used as hemostatic material and for wound healing applications.
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Affiliation(s)
- Xiaochen Cheng
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Ziyu Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Chengbo Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Lejun Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Mazhar Ali Raja
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
| | - Chenguang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, P. R. China
- * E-mail:
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40
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Clements KA, Acevedo-Jake AM, Walker DR, Hartgerink JD. Glycine Substitutions in Collagen Heterotrimers Alter Triple Helical Assembly. Biomacromolecules 2017; 18:617-624. [DOI: 10.1021/acs.biomac.6b01808] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katherine A. Clements
- Department of Chemistry, Rice University, 6100
Main Street, Houston, Texas 77005, United States
| | - Amanda M. Acevedo-Jake
- 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
| | - Jeffrey D. Hartgerink
- Department of Chemistry, Rice University, 6100
Main Street, Houston, Texas 77005, United States
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41
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Chhum P, Yu H, An B, Doyon BR, Lin YS, Brodsky B. Consequences of Glycine Mutations in the Fibronectin-binding Sequence of Collagen. J Biol Chem 2016; 291:27073-27086. [PMID: 27799304 DOI: 10.1074/jbc.m116.753566] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Indexed: 11/06/2022] Open
Abstract
Collagen and fibronectin (Fn) are two key extracellular matrix proteins, which are known to interact and jointly shape matrix structure and function. Most proteins that interact with collagen bind only to the native triple-helical form, whereas Fn is unusual in binding strongly to denatured collagen and more weakly to native collagen. The consequences of replacing a Gly by Ser at each position in the required (Gly-Xaa-Yaa)6 Fn-binding sequence are probed here, using model peptides and a recombinant bacterial collagen system. Fluorescence polarization and solid-state assays indicated that Gly replacements at four sites within the Fn-binding sequence led to decreased Fn binding to denatured collagen. Molecular dynamics simulations showed these Gly replacements interfered with the interaction of a collagen β-strand with the β-sheet structure of Fn modules seen in the high resolution crystal structure. Whereas previous studies showed that Gly to Ser mutations within an integrin-binding site caused no major structural perturbations, mutations within the Fn-binding site caused the triple helix to become highly sensitive to trypsin digestion. This trypsin susceptibility is consistent with the significant local unfolding and loss of hydrogen bonding seen in molecular dynamics simulations. Protease sensitivity resulting from mutations in the Fn-binding sequence could lead to degradation of type I collagen, early embryonic lethality, and the scarcity of reported osteogenesis imperfecta mutations in this region.
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Affiliation(s)
| | - Hongtao Yu
- From the Departments of Biomedical Engineering and.,Chemistry, Tufts University, Medford, Massachusetts 02155
| | - Bo An
- From the Departments of Biomedical Engineering and
| | | | - Yu-Shan Lin
- Chemistry, Tufts University, Medford, Massachusetts 02155
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42
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Yigit S, Yu H, An B, Hamaia S, Farndale RW, Kaplan DL, Lin YS, Brodsky B. Mapping the Effect of Gly Mutations in Collagen on α2β1 Integrin Binding. J Biol Chem 2016; 291:19196-207. [PMID: 27432884 PMCID: PMC5009287 DOI: 10.1074/jbc.m116.726182] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
The replacement of one Gly in the essential repeating tripeptide sequence of the type I collagen triple helix results in the dominant hereditary bone disorder osteogenesis imperfecta. The mechanism leading to pathology likely involves misfolding and autophagy, although it has been hypothesized that some mutations interfere with known collagen interactions. Here, the effect of Gly replacements within and nearby the integrin binding GFPGER sequence was investigated using a recombinant bacterial collagen system. When a six-triplet human type I collagen sequence containing GFPGER was introduced into a bacterial collagen-like protein, this chimeric protein bound to integrin. Constructs with Gly to Ser substitutions within and nearby the inserted human sequence still formed a trypsin-resistant triple helix, suggesting a small local conformational perturbation. Gly to Ser mutations within the two Gly residues in the essential GFPGER sequence prevented integrin binding and cell attachment as predicted from molecular dynamics studies of the complex. Replacement of Gly residues C-terminal to GFPGER did not affect integrin binding. In contrast, Gly replacements N-terminal to the GFPGER sequence, up to four triplets away, decreased integrin binding and cell adhesion. This pattern suggests either an involvement of the triplets N-terminal to GFPGER in initial binding or a propagation of the perturbation of the triple helix C-terminal to a mutation site. The asymmetry in biological consequences relative to the mutation site may relate to the observed pattern of osteogenesis imperfecta mutations near the integrin binding site.
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Affiliation(s)
- Sezin Yigit
- From the Departments of Biomedical Engineering and Chemistry, Tufts University, Medford, Massachusetts 02155 and
| | - Hongtao Yu
- From the Departments of Biomedical Engineering and Chemistry, Tufts University, Medford, Massachusetts 02155 and
| | - Bo An
- From the Departments of Biomedical Engineering and
| | - Samir Hamaia
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | | | - Yu-Shan Lin
- Chemistry, Tufts University, Medford, Massachusetts 02155 and
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43
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Gaggar A, Weathington N. Bioactive extracellular matrix fragments in lung health and disease. J Clin Invest 2016; 126:3176-84. [PMID: 27584731 DOI: 10.1172/jci83147] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The extracellular matrix (ECM) is the noncellular component critical in the maintenance of organ structure and the regulation of tissue development, organ structure, and cellular signaling. The ECM is a dynamic entity that undergoes continuous degradation and resynthesis. In addition to compromising structure, degradation of the ECM can liberate bioactive fragments that cause cellular activation and chemotaxis of a variety of cells. These fragments are termed matrikines, and their cellular activities are sentinel in the development and progression of tissue injury seen in chronic lung disease. Here, we discuss the matrikines that are known to be active in lung biology and their roles in lung disease. We also consider the use of matrikines as disease markers and potential therapeutic targets in lung disease.
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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45
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Zhang Y, Herling M, Chenoweth DM. General Solution for Stabilizing Triple Helical Collagen. J Am Chem Soc 2016; 138:9751-4. [DOI: 10.1021/jacs.6b03823] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yitao Zhang
- Department of Chemistry, University of Pennsylvania, 231 South
34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Madison Herling
- Department of Chemistry, University of Pennsylvania, 231 South
34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South
34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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46
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Aziz J, Shezali H, Radzi Z, Yahya NA, Abu Kassim NH, Czernuszka J, Rahman MT. Molecular Mechanisms of Stress-Responsive Changes in Collagen and Elastin Networks in Skin. Skin Pharmacol Physiol 2016; 29:190-203. [PMID: 27434176 DOI: 10.1159/000447017] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022]
Abstract
Collagen and elastin networks make up the majority of the extracellular matrix in many organs, such as the skin. The mechanisms which are involved in the maintenance of homeostatic equilibrium of these networks are numerous, involving the regulation of genetic expression, growth factor secretion, signalling pathways, secondary messaging systems, and ion channel activity. However, many factors are capable of disrupting these pathways, which leads to an imbalance of homeostatic equilibrium. Ultimately, this leads to changes in the physical nature of skin, both functionally and cosmetically. Although various factors have been identified, including carcinogenesis, ultraviolet exposure, and mechanical stretching of skin, it was discovered that many of them affect similar components of regulatory pathways, such as fibroblasts, lysyl oxidase, and fibronectin. Additionally, it was discovered that the various regulatory pathways intersect with each other at various stages instead of working independently of each other. This review paper proposes a model which elucidates how these molecular pathways intersect with one another, and how various internal and external factors can disrupt these pathways, ultimately leading to a disruption in collagen and elastin networks.
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Affiliation(s)
- Jazli Aziz
- Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
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47
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A novel COL11A1 missense mutation in siblings with non-ocular Stickler syndrome. Hum Genome Var 2016; 3:16003. [PMID: 27081569 PMCID: PMC4823386 DOI: 10.1038/hgv.2016.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/09/2022] Open
Abstract
Stickler syndrome (STL) is an autosomal, dominantly inherited, clinically variable and genetically heterogeneous connective tissue disorder characterized by ocular, auditory, orofacial and skeletal abnormalities. We conducted targeted resequencing using a next-generation sequencer for molecular diagnosis of a 2-year-old girl who was clinically suspected of having STL with Pierre Robin sequence. We detected a novel heterozygous missense mutation, NM_001854.3:n.4838G>A [NM_001854.3 (COL11A1_v001):c.4520G>A], in COL11A1, resulting in a Gly to Asp substitution at position 1507 [NM_001854.3(COL11A1_i001)] within one of the collagen-like domains of the triple helical region. The same mutation was detected in her 4-year-old brother with cleft palate and high-frequency sensorineural hearing loss.
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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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49
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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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Yigit S, Dinjaski N, Kaplan DL. Fibrous proteins: At the crossroads of genetic engineering and biotechnological applications. Biotechnol Bioeng 2015; 113:913-29. [PMID: 26332660 DOI: 10.1002/bit.25820] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/27/2015] [Accepted: 08/25/2015] [Indexed: 12/30/2022]
Abstract
Fibrous proteins, such as silk, elastin and collagen are finding broad impact in biomaterial systems for a range of biomedical and industrial applications. Some of the key advantages of biosynthetic fibrous proteins compared to synthetic polymers include the tailorability of sequence, protein size, degradation pattern, and mechanical properties. Recombinant DNA production and precise control over genetic sequence of these proteins allows expansion and fine tuning of material properties to meet the needs for specific applications. We review current approaches in the design, cloning, and expression of fibrous proteins, with a focus on strategies utilized to meet the challenges of repetitive fibrous protein production. We discuss recent advances in understanding the fundamental basis of structure-function relationships and the designs that foster fibrous protein self-assembly towards predictable architectures and properties for a range of applications. We highlight the potential of functionalization through genetic engineering to design fibrous protein systems for biotechnological and biomedical applications.
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Affiliation(s)
- Sezin Yigit
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts, 02155.,Department of Chemistry, Tufts University, Somerville, Massachusetts, 02145
| | - Nina Dinjaski
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts, 02155.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - David L Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts, 02155.
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