1
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Zhao T, Ma H, Liu Y, Chen Z, Shi Q, Ning L. Interfacial interactions between spider silk protein and cellulose studied by molecular dynamics simulation. J Mol Model 2024; 30:156. [PMID: 38693294 DOI: 10.1007/s00894-024-05945-w] [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: 07/28/2023] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
CONTEXT Due to their excellent biocompatibility and degradability, cellulose/spider silk protein composites hold a significant value in biomedical applications such as tissue engineering, drug delivery, and medical dressings. The interfacial interactions between cellulose and spider silk protein affect the properties of the composite. Therefore, it is important to understand the interfacial interactions between spider silk protein and cellulose to guide the design and optimization of composites. The study of the adsorption of protein on specific surfaces of cellulose crystal can be very complex using experimental methods. Molecular dynamics simulations allow the exploration of various physical and chemical changes at the atomic level of the material and enable an atomic description of the interactions between cellulose crystal planes and spider silk protein. In this study, molecular dynamics simulations were employed to investigate the interfacial interactions between spider silk protein (NTD) and cellulose surfaces. Findings of RMSD, RMSF, and secondary structure showed that the structure of NTD proteins remained unchanged during the adsorption process. Cellulose contact numbers and hydrogen bonding trends on different crystalline surfaces suggest that van der Waals forces and hydrogen bonding interactions drive the binding of proteins to cellulose. These findings reveal the interaction between cellulose and protein at the molecular level and provide theoretical guidance for the design and synthesis of cellulose/spider silk protein composites. METHODS MD simulations were all performed using the GROMACS-5.1 software package and run with CHARMM36 carbohydrate force field. Molecular dynamics simulations were performed for 500 ns for the simulated system.
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Affiliation(s)
- Tengfei Zhao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Huaiqin Ma
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Yuxi Liu
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Zhenjuan Chen
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Qingwen Shi
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China
| | - Lulu Ning
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, College of Bioresource Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, People's Republic of China.
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2
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Oktaviani NA, Malay AD, Matsugami A, Hayashi F, Numata K. Unusual p Ka Values Mediate the Self-Assembly of Spider Dragline Silk Proteins. Biomacromolecules 2023; 24:1604-1616. [PMID: 36990448 PMCID: PMC10091414 DOI: 10.1021/acs.biomac.2c01344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Spider dragline silk is a remarkably tough biomaterial and composed primarily of spidroins MaSp1 and MaSp2. During fiber self-assembly, the spidroin N-terminal domains (NTDs) undergo rapid dimerization in response to a pH gradient. However, obtaining a detailed understanding of this mechanism has been hampered by a lack of direct evidence regarding the protonation states of key ionic residues. Here, we elucidated the solution structures of MaSp1 and MaSp2 NTDs from Trichonephila clavipes and determined the experimental pKa values of conserved residues involved in dimerization using NMR. Surprisingly, we found that the Asp40 located on an acidic cluster protonates at an unusually high pH (∼6.5-7.1), suggesting the first step in the pH response. Then, protonation of Glu119 and Glu79 follows, with pKas above their intrinsic values, contributing toward stable dimer formation. We propose that exploiting the atypical pKa values is a strategy to achieve tight spatiotemporal control of spider silk self-assembly.
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Affiliation(s)
- Nur Alia Oktaviani
- Biomacromolecules Research Team, RIKEN Center for the Sustainable Resource Sciences, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ali D Malay
- Biomacromolecules Research Team, RIKEN Center for the Sustainable Resource Sciences, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for the Sustainable Resource Sciences, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku, Katsura, Kyoto 615-8510, Japan
- Institute for Advanced Bioscience, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
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3
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Sarr M, Kitoka K, Walsh-White KA, Kaldmäe M, Metlāns R, Tārs K, Mantese A, Shah D, Landreh M, Rising A, Johansson J, Jaudzems K, Kronqvist N. The dimerization mechanism of the N-terminal domain of spider silk proteins is conserved despite extensive sequence divergence. J Biol Chem 2022; 298:101913. [PMID: 35398358 PMCID: PMC9097459 DOI: 10.1016/j.jbc.2022.101913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/09/2022] Open
Abstract
The N-terminal (NT) domain of spider silk proteins (spidroins) is crucial for their storage at high concentrations and also regulates silk assembly. NTs from the major ampullate spidroin (MaSp) and the minor ampullate spidroin are monomeric at neutral pH and confer solubility to spidroins, whereas at lower pH, they dimerize to interconnect spidroins in a fiber. This dimerization is known to result from modulation of electrostatic interactions by protonation of well-conserved glutamates, although it is undetermined if this mechanism applies to other spidroin types as well. Here, we determine the solution and crystal structures of the flagelliform spidroin NT, which shares only 35% identity with MaSp NT, and investigate the mechanisms of its dimerization. We show that flagelliform spidroin NT is structurally similar to MaSp NT and that the electrostatic intermolecular interaction between Asp 40 and Lys 65 residues is conserved. However, the protonation events involve a different set of residues than in MaSp, indicating that an overall mechanism of pH-dependent dimerization is conserved but can be mediated by different pathways in different silk types.
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Affiliation(s)
- Médoune Sarr
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Kristine Kitoka
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, 1006, Latvia
| | - Kellie-Ann Walsh-White
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Rimants Metlāns
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, 1006, Latvia
| | - Kaspar Tārs
- Latvian Biomedical Research and Study Centre, Riga, 1067, Latvia
| | | | - Dipen Shah
- ZoBio BV, J.H. Oortweg 19, 2333CH Leiden, the Netherlands
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Anna Rising
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Biosciences and Nutrition, Neo, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, 1006, Latvia
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Karolinska Institutet, 141 83 Huddinge, Sweden; Department of Biosciences and Nutrition, Neo, Karolinska Institutet, 141 83 Huddinge, Sweden.
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4
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Li X, Qi X, Cai YM, Sun Y, Wen R, Zhang R, Johansson J, Meng Q, Chen G. Customized Flagelliform Spidroins Form Spider Silk-like Fibers at pH 8.0 with Outstanding Tensile Strength. ACS Biomater Sci Eng 2021; 8:119-127. [PMID: 34908395 PMCID: PMC8753598 DOI: 10.1021/acsbiomaterials.1c01354] [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] [Indexed: 11/29/2022]
Abstract
Spider flagelliform silk shows the best extensibility among various types of silk, but its biomimetic preparation has not been much studied. Herein, five customized flagelliform spidroins (FlSps: S and NTDFl-Sn-CTDFl, n = 1-4), in which the repetitive region (S) and N-/C- terminal domains (NTDFl and CTDFl) are from the same spidroin and spider species, were produced recombinantly. The recombinant spidroins with terminal domains were able to form silk-like fibers with diameters of ∼5 μm by manual pulling at pH 8.0, where the secondary structure transformation occurred. The silk-like fibers from NTDFl-S4-CTDFl showed the highest tensile strength (∼250 MPa), while those ones with 1-3 S broke at a similar stress (∼180 MPa), suggesting that increasing the amounts of the repetitive region can improve the tensile strength, but a certain threshold might need to be reached. This study shows successful preparation of flagelliform silk-like fibers with good mechanical properties, providing general insights into efficient biomimetic preparations of spider silks.
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Affiliation(s)
- Xue Li
- Department of Medical Ultrasound, Shanghai Tenth People's Hospital, Ultrasound Research and Education Institute, Tongji University Cancer Center, Shanghai Engineering Research Center of Ultrasound Diagnosis and Treatment, Tongji University School of Medicine, 200092 Shanghai, China.,Institute of Biological Sciences and Biotechnology, Donghua University, 201620 Shanghai, China
| | - Xingmei Qi
- The Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yu-Ming Cai
- Institute for Life Sciences, University of Southampton, SO17 1BJ Southampton, Hampshire, U.K
| | - Yuan Sun
- Institute of Biological Sciences and Biotechnology, Donghua University, 201620 Shanghai, China
| | - Rui Wen
- Institute of Biological Sciences and Biotechnology, Donghua University, 201620 Shanghai, China
| | - Rui Zhang
- Department of Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 14157 Huddinge, Sweden
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, 201620 Shanghai, China
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 14157 Huddinge, Sweden
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5
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Correa-Garhwal SM, Babb PL, Voight BF, Hayashi CY. Golden orb-weaving spider (Trichonephila clavipes) silk genes with sex-biased expression and atypical architectures. G3-GENES GENOMES GENETICS 2021; 11:6044138. [PMID: 33561241 PMCID: PMC8022711 DOI: 10.1093/g3journal/jkaa039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/05/2020] [Indexed: 11/29/2022]
Abstract
Spider silks are renowned for their high-performance mechanical properties. Contributing to these properties are proteins encoded by the spidroin (spider fibroin) gene family. Spidroins have been discovered mostly through cDNA studies of females based on the presence of conserved terminal regions and a repetitive central region. Recently, genome sequencing of the golden orb-web weaver, Trichonephila clavipes, provided a complete picture of spidroin diversity. Here, we refine the annotation of T. clavipes spidroin genes including the reclassification of some as non-spidroins. We rename these non-spidroins as spidroin-like (SpL) genes because they have repetitive sequences and amino acid compositions like spidroins, but entirely lack the archetypal terminal domains of spidroins. Insight into the function of these spidroin and SpL genes was then examined through tissue- and sex-specific gene expression studies. Using qPCR, we show that some silk genes are upregulated in male silk glands compared to females, despite males producing less silk in general. We also find that an enigmatic spidroin that lacks a spidroin C-terminal domain is highly expressed in silk glands, suggesting that spidroins could assemble into fibers without a canonical terminal region. Further, we show that two SpL genes are expressed in silk glands, with one gene highly evolutionarily conserved across species, providing evidence that particular SpL genes are important to silk production. Together, these findings challenge long-standing paradigms regarding the evolutionary and functional significance of the proteins and conserved motifs essential for producing spider silks.
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Affiliation(s)
- Sandra M Correa-Garhwal
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Paul L Babb
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl Y Hayashi
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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6
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Wang J, Yuan W, Qin R, Fan T, Fan JS, Huang W, Yang D, Lin Z. Self-assembly of tubuliform spidroins driven by hydrophobic interactions among terminal domains. Int J Biol Macromol 2020; 166:1141-1148. [PMID: 33157141 DOI: 10.1016/j.ijbiomac.2020.10.269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 11/26/2022]
Abstract
Spider silk has remarkable physical and biocompatible properties. Investigation of structure-function relationship and self-assembly process of spidroins is necessary for uncovering the mechanism of silk fiber formation. Nevertheless, how the terminal domains initiate self-assembly of soluble tubuliform spidroins to form solid eggcase silk is still not fully understood. Here we investigate the roles of both terminal domains of tubuliform spidroin 1 (TuSp1) in the silk fiber formation. We found that interactions among the terminal domains drive rapid TuSp1 self-assembly and fiber formation, which is insensitive to pH changes from 6.0 to 7.0. These interactions also contribute to the spidroin chain alignment in fiber formation upon shear-force exposure. Structural analysis and site-directed mutagenesis identified eight critical surface-exposed residues involved in hydrophobic interactions among terminal domains. Spidroins with single-point mutations of these residues fail to form intermediate micelle-like structures. The structural docking model indicates that multiple terminal domains of TuSp1 may interact with each other based on hydrophobic interactions and surface complementarity, which may lead to forming the surface of the micelle-like structure. Our results provide new insights into the structural mechanism of eggcase silk formation and the basis for designing and producing novel biomaterials derived from spider eggcase silk.
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Affiliation(s)
- Jingxia Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, PR China
| | - Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, PR China
| | - Ruiqi Qin
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, PR China
| | - Tiantian Fan
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, PR China
| | - Jing-Song Fan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Weidong Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia, 750004, PR China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin 300072, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, PR China.
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7
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Poddar H, Breitling R, Takano E. Towards engineering and production of artificial spider silk using tools of synthetic biology. ENGINEERING BIOLOGY 2020; 4:1-6. [PMID: 36970229 PMCID: PMC9996717 DOI: 10.1049/enb.2019.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
Spider silk is one of the strongest biomaterials available in nature. Its mechanical properties make it a good candidate for applications in various fields ranging from protective armour to bandages for wound dressing to coatings for medical implants. Spider silk is formed by an intricate arrangement of spidroins, which are extremely large proteins containing long stretches of repeating segments rich in alanine and glycine. A large amount of research has been directed towards harnessing the spectacular potential of spider silks and using them for different applications. The interdisciplinary approach of synthetic biology is an ideal tool to study these spider silk proteins and work towards the engineering and production of synthetic spider silk. This review aims to highlight the recent progress that has been made in the study of spider silk proteins using different branches of synthetic biology. Here, the authors discuss the different computational approaches, directed evolution techniques and various expression platforms that have been tested for the successful production of spider silk. Future challenges facing the field and possible solutions offered by synthetic biology are also discussed.
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Affiliation(s)
- Hashwardhan Poddar
- Faculty of Science and Engineering, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM The University of Manchester Manchester M1 7DN UK
| | - Rainer Breitling
- Faculty of Science and Engineering, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM The University of Manchester Manchester M1 7DN UK
| | - Eriko Takano
- Faculty of Science and Engineering, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM The University of Manchester Manchester M1 7DN UK
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8
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Peng CA, Kozubowski L, Marcotte WR. Advances in Plant-Derived Scaffold Proteins. FRONTIERS IN PLANT SCIENCE 2020; 11:122. [PMID: 32161608 PMCID: PMC7052361 DOI: 10.3389/fpls.2020.00122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/27/2020] [Indexed: 05/13/2023]
Abstract
Scaffold proteins form critical biomatrices that support cell adhesion and proliferation for regenerative medicine and drug screening. The increasing demand for such applications urges solutions for cost effective and sustainable supplies of hypoallergenic and biocompatible scaffold proteins. Here, we summarize recent efforts in obtaining plant-derived biosynthetic spider silk analogue and the extracellular matrix protein, collagen. Both proteins are composed of a large number of tandem block repeats, which makes production in bacterial hosts challenging. Furthermore, post-translational modification of collagen is essential for its function which requires co-transformation of multiple copies of human prolyl 4-hydroxylase. We discuss our perspectives on how the GAANTRY system could potentially assist the production of native-sized spider dragline silk proteins and prolyl hydroxylated collagen. The potential of recombinant scaffold proteins in drug delivery and drug discovery is also addressed.
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9
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Heiby JC, Goretzki B, Johnson CM, Hellmich UA, Neuweiler H. Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk. Nat Commun 2019; 10:4378. [PMID: 31558722 PMCID: PMC6763431 DOI: 10.1038/s41467-019-12365-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023] Open
Abstract
Web spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of core methionines serve to mobilize the fold, which can thereby access various conformations and adapt the association interface for tight binding. Methionine in a hydrophobic core equips a protein with the capacity to dynamically change shape and thus to optimize its function. Spider silk is of interest in material science research. Here the authors show that the tight binding of a spider silk protein domain relies on the amino acid methionine, which is abundant in the domain core where it facilitates dynamic shape adaption of the binding interface.
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Affiliation(s)
- Julia C Heiby
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany.,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Christopher M Johnson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes-Gutenberg-University Mainz, Johann-Joachim Becherweg 30, 55128, Mainz, Germany. .,Center for Biomolecular Magnetic Resonance, Goethe-University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
| | - Hannes Neuweiler
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074, Würzburg, Germany.
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10
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Jiang W, Askarieh G, Shkumatov A, Hedhammar M, Knight SD. Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:618-627. [DOI: 10.1107/s2059798319007253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/20/2019] [Indexed: 11/11/2022]
Abstract
Spider silk is a biomaterial with exceptional mechanical toughness, and there is great interest in developing biomimetic methods to produce engineered spider silk-based materials. However, the mechanisms that regulate the conversion of spider silk proteins (spidroins) from highly soluble dope into silk are not completely understood. The N-terminal domain (NT) of Euprosthenops australis dragline silk protein undergoes conformational and quaternary-structure changes from a monomer at a pH above 7 to a homodimer at lower pH values. Conversion from the monomer to the dimer requires the protonation of three conserved glutamic acid residues, resulting in a low-pH `locked' dimer stabilized by symmetric electrostatic interactions at the poles of the dimer. The detailed molecular events during this transition are still unresolved. Here, a 2.1 Å resolution crystal structure of an NT T61A mutant in an alternative, asymmetric, dimer form in which the electrostatic interactions at one of the poles are dramatically different from those in symmetrical dimers is presented. A similar asymmetric dimer structure from dragline silk of Nephila clavipes has previously been described. It is suggested that asymmetric dimers represent a conserved intermediate state in spider silk formation, and a revised `lock-and-trigger' mechanism for spider silk formation is presented.
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11
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McGill M, Holland GP, Kaplan DL. Experimental Methods for Characterizing the Secondary Structure and Thermal Properties of Silk Proteins. Macromol Rapid Commun 2019; 40:e1800390. [PMID: 30073740 PMCID: PMC6425979 DOI: 10.1002/marc.201800390] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 06/16/2018] [Indexed: 12/17/2022]
Abstract
Silk proteins are biopolymers produced by spinning organisms that have been studied extensively for applications in materials engineering, regenerative medicine, and devices due to their high tensile strength and extensibility. This remarkable combination of mechanical properties arises from their unique semi-crystalline secondary structure and block copolymer features. The secondary structure of silks is highly sensitive to processing, and can be manipulated to achieve a wide array of material profiles. Studying the secondary structure of silks is therefore critical to understanding the relationship between structure and function, the strength and stability of silk-based materials, and the natural fiber synthesis process employed by spinning organisms. However, silks present unique challenges to structural characterization due to high-molecular-weight protein chains, repetitive sequences, and heterogeneity in intra- and interchain domain sizes. Here, experimental techniques used to study the secondary structure of silks, the information attainable from these techniques, and the limitations associated with them are reviewed. Ultimately, the appropriate utilization of a suite of techniques discussed here will enable detailed characterization of silk-based materials, from studying fundamental processing-structure-function relationships to developing commercially useful quality control assessments.
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Affiliation(s)
- Meghan McGill
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
| | - Gregory P. Holland
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155, USA
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12
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Conservation of folding and association within a family of spidroin N-terminal domains. Sci Rep 2017; 7:16789. [PMID: 29196631 PMCID: PMC5711802 DOI: 10.1038/s41598-017-16881-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/17/2017] [Indexed: 11/25/2022] Open
Abstract
Web spiders synthesize silk fibres, nature’s toughest biomaterial, through the controlled assembly of fibroin proteins, so-called spidroins. The highly conserved spidroin N-terminal domain (NTD) is a pH-driven self-assembly device that connects spidroins to super-molecules in fibres. The degree to which forces of self-assembly is conserved across spider glands and species is currently unknown because quantitative measures are missing. Here, we report the comparative investigation of spidroin NTDs originating from the major ampullate glands of the spider species Euprosthenops australis, Nephila clavipes, Latrodectus hesperus, and Latrodectus geometricus. We characterized equilibrium thermodynamics and kinetics of folding and self-association using dynamic light scattering, stopped-flow fluorescence and circular dichroism spectroscopy in combination with thermal and chemical denaturation experiments. We found cooperative two-state folding on a sub-millisecond time scale through a late transition state of all four domains. Stability was compromised by repulsive electrostatic forces originating from clustering of point charges on the NTD surface required for function. pH-driven dimerization proceeded with characteristic fast kinetics yielding high affinities. Results showed that energetics and kinetics of NTD self-assembly are highly conserved across spider species despite the different silk mechanical properties and web geometries they produce.
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Efficient protein production inspired by how spiders make silk. Nat Commun 2017; 8:15504. [PMID: 28534479 PMCID: PMC5457526 DOI: 10.1038/ncomms15504] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/04/2017] [Indexed: 01/05/2023] Open
Abstract
Membrane proteins are targets of most available pharmaceuticals, but they are difficult to produce recombinantly, like many other aggregation-prone proteins. Spiders can produce silk proteins at huge concentrations by sequestering their aggregation-prone regions in micellar structures, where the very soluble N-terminal domain (NT) forms the shell. We hypothesize that fusion to NT could similarly solubilize non-spidroin proteins, and design a charge-reversed mutant (NT*) that is pH insensitive, stabilized and hypersoluble compared to wild-type NT. NT*-transmembrane protein fusions yield up to eight times more of soluble protein in Escherichia coli than fusions with several conventional tags. NT* enables transmembrane peptide purification to homogeneity without chromatography and manufacture of low-cost synthetic lung surfactant that works in an animal model of respiratory disease. NT* also allows efficient expression and purification of non-transmembrane proteins, which are otherwise refractory to recombinant production, and offers a new tool for reluctant proteins in general.
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Sonati S, Bhutoria S, Prabhakaran M, Acharya SA. Influence of semisynthetic modification of the scaffold of a contact domain of HbS on polymerization: role of flexible surface topology in polymerization inhibition. J Biomol Struct Dyn 2017; 36:689-700. [PMID: 28278759 DOI: 10.1080/07391102.2017.1294111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A new variant of HbS, HbS-Einstein with a deletion of segment α23-26 in the B-helix, has been assembled by semisynthetic approach. B-helix of the α chain of cis αβ-dimer of HbS plays dominant role in the quinary interactions of deoxy HbS dimer. This B-helix is the primary scaffold that provides the orientation for the side chains of contact residues of this intermolecular contact domain. The design of HbS-Einstein has been undertaken to map the influence of perturbation of molecular surface topology and the flexibility of surface residues in the polymerization. The internal deletion exerts a strong inhibitory influence on Val-6 (β)-dependent polymerization, comparable to single contact site mutations and not for complete neutralization of Val-6(β)-dependent polymerization. The scaffold modification in cis-dimer is inhibitory, and is without any effect when present on the trans dimer. The flexibility changes in the surface topology in the region of scaffold modification apparently counteracts the intrinsic polymerization potential of the molecule. The inhibition is close to that of Le Lamentin mutation [His-20 (α) → Gln] wherein a mutation engineered without much change in flexibility of the contact domain. Interestingly, the chimeric HbS with swine-human chimeric α chain with multiple non-conservative mutations completely inhibits the Val-6(β)-dependent polymerization. The deformabilities of surface topology of chimeric HbS are comparable to HbS in spite of the multiple contact site mutations in the α-chain. We conclude that the design of antisickling Hbs for gene therapy of sickle cell disease should involve multiple mutations of intermolecular contact sites.
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Affiliation(s)
- Srinivasulu Sonati
- a Division of Hematology , Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461 , USA
| | - Savita Bhutoria
- a Division of Hematology , Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461 , USA
| | - Muthuchidambaran Prabhakaran
- a Division of Hematology , Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461 , USA
| | - Seetharama A Acharya
- a Division of Hematology , Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461 , USA.,b Department(s) of Medicine and of Physiology and Biophysics , Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461 , USA
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