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Kiya M, Shiga S, Ding P, Koide S, Makabe K. β-Strand-mediated Domain-swapping in the Absence of Hydrophobic Core Repacking. J Mol Biol 2024; 436:168405. [PMID: 38104859 DOI: 10.1016/j.jmb.2023.168405] [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: 07/31/2023] [Revised: 11/03/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Domain swapping is a process wherein a portion of a protein is exchanged with its counterpart in another copy of the molecule, resulting in the formation of homo-oligomers with concomitant repacking of a hydrophobic core. Here, we report domain swapping triggered upon modifying a β-hairpin sequence within a single-layer β-sheet (SLB) of a model protein, OspA that did not involve the formation of a reorganized hydrophobic core. The replacement of two β-hairpin sequences with a Gly-Gly and shorteing of a β-hairpin resulted in a protein that formed two distinct crystal structures under similar conditions: one was monomeric, similar to the parental molecule, whereas the other was a domain-swapped dimer, mediated by an intermolecular β-sheet in the SLB portion. Based on the dimer interface structure, we replaced the Gly-Gly sequence with three-residue sequences that enable the formation of a consecutive intermolecular β-sheet, including the Cys-Thr-Cys sequence that formed a stable disulfide-linked dimer. These results provide new insights into protein folding, evolution, and the designability of protein structure.
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Affiliation(s)
- Mikoto Kiya
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shota Shiga
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Peiwei Ding
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, and Perlmutter Cancer Center at NYU Langone Health, New York, NY 10016, USA
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan.
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2
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Jędrzejewska H, Wielgus E, Kaźmierski S, Rogala H, Wierzbicki M, Wróblewska A, Pawlak T, Potrzebowski MJ, Szumna A. Porous Molecular Capsules as Non-Polymeric Transducers of Mechanical Forces to Mechanophores. Chemistry 2020; 26:1558-1566. [PMID: 31691377 DOI: 10.1002/chem.201904024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 11/05/2022]
Abstract
Mechanical grinding/milling can be regarded as historically the first technology for changing the properties of matter. Mechanically activated molecular units (mechanophores) can be present in various structures: polymers, macromolecules, or small molecules. However, only polymers have been reported to effectively transduce energy to mechanophores, which induces breakage of covalent bonds. In this paper, a second possibility is presented-molecular capsules as stress-sensitive units. Mechanochemical encapsulation of fullerenes in cystine-based covalent capsules indicates that complexation takes place in the solid state, despite the fact that the capsules do not possess large enough entrance portals. By using a set of solvent-free MALDI (sf-MALDI) and solid-state NMR (ss-NMR) experiments, it has been proven that encapsulation proceeds during milling and in this process hydrazones and disulfides get activated for breakage, exchange, and re-forming. The capsules are porous and therefore prone to collapse under solvent-free conditions and their conformational rigidity promotes the collapse by the breaking of covalent bonds.
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Affiliation(s)
- Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Halina Rogala
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Michał Wierzbicki
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Aneta Wróblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences, M. Kasprzaka 44/52, 01-224, Warsaw, Poland
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3
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Kaiser CJO, Peters C, Schmid PWN, Stavropoulou M, Zou J, Dahiya V, Mymrikov EV, Rockel B, Asami S, Haslbeck M, Rappsilber J, Reif B, Zacharias M, Buchner J, Weinkauf S. The structure and oxidation of the eye lens chaperone αA-crystallin. Nat Struct Mol Biol 2019; 26:1141-1150. [PMID: 31792453 PMCID: PMC7115824 DOI: 10.1038/s41594-019-0332-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/10/2019] [Indexed: 11/08/2022]
Abstract
The small heat shock protein αA-crystallin is a molecular chaperone important for the optical properties of the vertebrate eye lens. It forms heterogeneous oligomeric ensembles. We determined the structures of human αA-crystallin oligomers by combining cryo-electron microscopy, cross-linking/mass spectrometry, NMR spectroscopy and molecular modeling. The different oligomers can be interconverted by the addition or subtraction of tetramers, leading to mainly 12-, 16- and 20-meric assemblies in which interactions between N-terminal regions are important. Cross-dimer domain-swapping of the C-terminal region is a determinant of αA-crystallin heterogeneity. Human αA-crystallin contains two cysteines, which can form an intramolecular disulfide in vivo. Oxidation in vitro requires conformational changes and oligomer dissociation. The oxidized oligomers, which are larger than reduced αA-crystallin and destabilized against unfolding, are active chaperones and can transfer the disulfide to destabilized substrate proteins. The insight into the structure and function of αA-crystallin provides a basis for understanding its role in the eye lens.
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Affiliation(s)
- Christoph J O Kaiser
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Carsten Peters
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Philipp W N Schmid
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Maria Stavropoulou
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Juan Zou
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vinay Dahiya
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Evgeny V Mymrikov
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute for Biochemistry and Molecular Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Beate Rockel
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Sam Asami
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Haslbeck
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Bernd Reif
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich at the Physics Department, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany.
| | - Sevil Weinkauf
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany.
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4
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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5
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Patil NA, Karas JA, Wade JD, Hossain MA, Tailhades J. Rapid Photolysis‐Mediated Folding of Disulfide‐Rich Peptides. Chemistry 2019; 25:8599-8603. [DOI: 10.1002/chem.201901334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Nitin A. Patil
- The Monash Biomedicine Discovery Institute 15 Innovation Walk Clayton VIC 3800 Australia
| | - John A. Karas
- Department of Pharmacology and TherapeuticsThe University of Melbourne Victoria 3010 Australia
| | - John D. Wade
- Department of Pharmacology and TherapeuticsThe University of Melbourne Victoria 3010 Australia
- The Florey Institute of Neuroscience and Mental HealthUniversity of Melbourne 30 Royal Parade, Parkville Victoria 3052 Australia
| | - Mohammed Akhter Hossain
- Department of Pharmacology and TherapeuticsThe University of Melbourne Victoria 3010 Australia
- The Florey Institute of Neuroscience and Mental HealthUniversity of Melbourne 30 Royal Parade, Parkville Victoria 3052 Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute 15 Innovation Walk Clayton VIC 3800 Australia
- EMBL AustraliaMonash University Clayton Victoria 3800 Australia
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6
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Rathore U, Purwar M, Vignesh VS, Das R, Kumar AA, Bhattacharyya S, Arendt H, DeStefano J, Wilson A, Parks C, La Branche CC, Montefiori DC, Varadarajan R. Bacterially expressed HIV-1 gp120 outer-domain fragment immunogens with improved stability and affinity for CD4-binding site neutralizing antibodies. J Biol Chem 2018; 293:15002-15020. [PMID: 30093409 DOI: 10.1074/jbc.ra118.005006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/20/2022] Open
Abstract
Protein minimization is an attractive approach for designing vaccines against rapidly evolving pathogens such as human immunodeficiency virus, type 1 (HIV-1), because it can help in focusing the immune response toward conserved conformational epitopes present on complex targets. The outer domain (OD) of HIV-1 gp120 contains epitopes for a large number of neutralizing antibodies and therefore is a primary target for structure-based vaccine design. We have previously designed a bacterially expressed outer-domain immunogen (ODEC) that bound CD4-binding site (CD4bs) ligands with 3-12 μm affinity and elicited a modest neutralizing antibody response in rabbits. In this study, we have optimized ODEC using consensus sequence design, cyclic permutation, and structure-guided mutations to generate a number of variants with improved yields, biophysical properties, stabilities, and affinities (KD of 10-50 nm) for various CD4bs targeting broadly neutralizing antibodies, including the germline-reverted version of the broadly neutralizing antibody VRC01. In contrast to ODEC, the optimized immunogens elicited high anti-gp120 titers in rabbits as early as 6 weeks post-immunization, before any gp120 boost was given. Following two gp120 boosts, sera collected at week 22 showed cross-clade neutralization of tier 1 HIV-1 viruses. Using a number of different prime/boost combinations, we have identified a cyclically permuted OD fragment as the best priming immunogen, and a trimeric, cyclically permuted gp120 as the most suitable boosting molecule among the tested immunogens. This study also provides insights into some of the biophysical correlates of improved immunogenicity.
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Affiliation(s)
- Ujjwal Rathore
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Mansi Purwar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | | | - Raksha Das
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Aditya Arun Kumar
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Sanchari Bhattacharyya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Heather Arendt
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Joanne DeStefano
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Aaron Wilson
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Christopher Parks
- the International AIDS Vaccine Initiative, Brooklyn, New York 11226, and
| | - Celia C La Branche
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - David C Montefiori
- the Department of Surgery, Duke University Medical Center, Durham, North Carolina 27707
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012,
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7
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Tanghe M, Danneels B, Last M, Beerens K, Stals I, Desmet T. Disulfide bridges as essential elements for the thermostability of lytic polysaccharide monooxygenase LPMO10C from Streptomyces coelicolor. Protein Eng Des Sel 2017; 30:401-408. [PMID: 28338903 DOI: 10.1093/protein/gzx014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/20/2017] [Indexed: 12/17/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are crucial components of cellulase mixtures but their stability has not yet been studied in detail, let alone been engineered for industrial applications. In this work, we have evaluated the importance of disulfide bridges for the thermodynamic stability of Streptomyces coelicolor LPMO10C. Interestingly, this enzyme was found to retain 34% of its activity after 2-h incubation at 80°C while its apparent melting temperature (Tm) is only 51°C. When its three disulfide bridges were broken, however, irreversible unfolding occurred and no residual activity could be detected after a similar heat treatment. Based on these findings, additional disulfide bridges were introduced, as predicted by computational tools (MOdelling of DIsulfide bridges in Proteins (MODiP) and Disulfide by Design (DbD)) and using the most flexible positions in the structure as target sites. Four out of 16 variants displayed an improvement in Tm, ranging from 2 to 9°C. Combining the positive mutations yielded additional improvements (up to 19°C) but aberrant unfolding patterns became apparent in some cases, resulting in a diminished capacity for heat resistance. Nonetheless, the best variant, a combination of A143C-P183C and S73C-A115C, displayed a 12°C increase in Tm and was able to retain and was able to retain no less than 60% of its activity after heat treatment.
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Affiliation(s)
- Magali Tanghe
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Barbara Danneels
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Matthias Last
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Koen Beerens
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Ingeborg Stals
- Industrial Catalysis and Adsorption Technology (INCAT), Faculty of Engineering and Architecture, Ghent University, Valentin Vaerwyckweg 1, B-9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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8
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Kier BL, Anderson JM, Andersen NH. Disulfide-Mediated β-Strand Dimers: Hyperstable β-Sheets Lacking Tertiary Interactions and Turns. J Am Chem Soc 2015; 137:5363-71. [PMID: 25835058 PMCID: PMC7450586 DOI: 10.1021/ja5117809] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Disulfide bonds between cysteine residues are essential to the structure and folding of many proteins. Yet their role in the design of structured peptides and proteins has frequently been limited to use as intrachain covalent staples that reinforce existing structure or induce knot-like conformations. In β-hairpins, their placement at non-H-bonding positions across antiparallel strands has proven useful for achieving fully folded positive controls. Here we report a new class of designed β-sheet peptide dimers with strand-central disulfides as a key element. We have found that the mere presence of a disulfide bond near the middle of a short peptide chain is sufficient to nucleate some antiparallel β-sheet structure; addition of β-capping units and other favorable cross-strand interactions yield hyperstable sheets. Strand-central cystines were found to be superior to the best designed reversing turns in terms of nucleating β-sheet structure formation. We have explored the limitations and possibilities of this technique (the use of disulfides as sheet nucleators), and we provide a set of rules and rationales for the application and further design of disulfide-tethered "turnless" β-sheets.
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Affiliation(s)
- Brandon L Kier
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Jordan M Anderson
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
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9
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Haworth NL, Wouters MA. Cross-strand disulfides in the non-hydrogen bonding site of antiparallel β-sheet (aCSDns): poised for biological switching. RSC Adv 2015. [DOI: 10.1039/c5ra10672a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
aCSDns are forbidden disulfides with protein redox-activity. Within the aCSDn structural motif, a cognate substrate of Trx-like enzymes, the disulfide bonds are strained and metastable, facilitating their role as redox-regulated protein switches.
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Affiliation(s)
- Naomi L. Haworth
- Life and Environmental Sciences
- Deakin University
- Geelong 3217
- Australia
- Victor Chang Cardiac Research Institute
| | - Merridee A. Wouters
- Olivia Newton-John Cancer Research Institute
- Heidelberg 3084
- Australia
- School of Cancer Medicine
- La Trobe University
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10
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A theoretical study of the stability of disulfide bridges in various β-sheet structures of protein segment models. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Singh P, Sharma L, Kulothungan SR, Adkar BV, Prajapati RS, Ali PSS, Krishnan B, Varadarajan R. Effect of signal peptide on stability and folding of Escherichia coli thioredoxin. PLoS One 2013; 8:e63442. [PMID: 23667620 PMCID: PMC3646739 DOI: 10.1371/journal.pone.0063442] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 04/03/2013] [Indexed: 11/19/2022] Open
Abstract
The signal peptide plays a key role in targeting and membrane insertion of secretory and membrane proteins in both prokaryotes and eukaryotes. In E. coli, recombinant proteins can be targeted to the periplasmic space by fusing naturally occurring signal sequences to their N-terminus. The model protein thioredoxin was fused at its N-terminus with malE and pelB signal sequences. While WT and the pelB fusion are soluble when expressed, the malE fusion was targeted to inclusion bodies and was refolded in vitro to yield a monomeric product with identical secondary structure to WT thioredoxin. The purified recombinant proteins were studied with respect to their thermodynamic stability, aggregation propensity and activity, and compared with wild type thioredoxin, without a signal sequence. The presence of signal sequences leads to thermodynamic destabilization, reduces the activity and increases the aggregation propensity, with malE having much larger effects than pelB. These studies show that besides acting as address labels, signal sequences can modulate protein stability and aggregation in a sequence dependent manner.
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Affiliation(s)
- Pranveer Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Likhesh Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Bharat V. Adkar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - P. Shaik Syed Ali
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Beena Krishnan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Chemical Biology Unit, Jawaharlal NehruCentre for Advanced Scientific Research, Jakkur, Bangalore, India
- * E-mail:
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12
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Conibear AC, Rosengren KJ, Daly NL, Henriques ST, Craik DJ. The cyclic cystine ladder in θ-defensins is important for structure and stability, but not antibacterial activity. J Biol Chem 2013; 288:10830-40. [PMID: 23430740 DOI: 10.1074/jbc.m113.451047] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
θ-Defensins are ribosomally synthesized cyclic peptides found in the leukocytes of some primate species and have promising applications as antimicrobial agents and scaffolds for peptide drugs. The cyclic cystine ladder motif, comprising a cyclic peptide backbone and three parallel disulfide bonds, is characteristic of θ-defensins. In this study, we explore the role of the cyclic peptide backbone and cystine ladder in the structure, stability, and activity of θ-defensins. θ-Defensin analogues with different numbers and combinations of disulfide bonds were synthesized and characterized in terms of their NMR solution structures, serum and thermal stabilities, and their antibacterial and membrane-binding activities. Whereas the structures and stabilities of the peptides were primarily dependent on the number and position of the disulfide bonds, their antibacterial and membrane-binding properties were dependent on the cyclic backbone. The results provide insights into the mechanism of action of θ-defensins and illustrate the potential of θ-defensin analogues as scaffolds for peptide drug design.
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Affiliation(s)
- Anne C Conibear
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland 4072, Australia
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13
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Haworth NL, Wouters MA. Between-strand disulfides: forbidden disulfides linking adjacent β-strands. RSC Adv 2013. [DOI: 10.1039/c3ra42486c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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14
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Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res 2012; 40:W288-93. [PMID: 22581768 PMCID: PMC3394260 DOI: 10.1093/nar/gks419] [Citation(s) in RCA: 449] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution. We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids. The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists. Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 Å from the full NMR structures. Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 Å RMS from the NMR rigid cores. The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server. The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD.
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15
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Zhang L, Chou CP, Moo-Young M. Disulfide bond formation and its impact on the biological activity and stability of recombinant therapeutic proteins produced by Escherichia coli expression system. Biotechnol Adv 2011; 29:923-9. [DOI: 10.1016/j.biotechadv.2011.07.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 07/17/2011] [Accepted: 07/21/2011] [Indexed: 11/28/2022]
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16
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Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Proteins 2011; 79:244-60. [PMID: 21058397 DOI: 10.1002/prot.22878] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity.
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Affiliation(s)
- S Indu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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17
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Zhang L, Moo-Young M, Chou CP. Molecular manipulation associated with disulfide bond formation to enhance the stability of recombinant therapeutic protein. Protein Expr Purif 2011; 75:28-39. [PMID: 20719248 DOI: 10.1016/j.pep.2010.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 08/10/2010] [Accepted: 08/11/2010] [Indexed: 11/17/2022]
Abstract
Cys²⁷ in the extracellular domain of human CD83 (hCD83ext), a potential therapeutic protein, was identified as a target for molecular manipulation. Two Escherichia coli strains of BL21(DE3) and Origami B(DE3), respectively, with a reducing and an oxidative cytoplasm were used as the expression host to produce the Cys²⁷ mutants. It was observed that Cys²⁷ was involved in the in vivo formation of intramolecular disulfide bonds when hCD83ext was expressed in Origami B(DE3). The Origami-derived protein products had a higher tendency than the BL21-derived counterparts for multimerization via the in vitro formation of intermolecular disulfide bonds. Various analyses were conducted to identify the structural differences among these mutant variants. Most importantly, molecular stability was enhanced by the Cys²⁷ mutations since the Cys²⁷ mutants derived from either BL21 or Origami were much less susceptible to degradation compared to wild-type hCD83ext. This study highlights the implications of aberrant disulfide bond formation on the production of therapeutic proteins.
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Affiliation(s)
- Lin Zhang
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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18
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Indu S, Kumar ST, Thakurela S, Gupta M, Bhaskara RM, Ramakrishnan C, Varadarajan R. Disulfide conformation and design at helix N-termini. Proteins 2010; 78:1228-42. [PMID: 19938155 PMCID: PMC7167797 DOI: 10.1002/prot.22641] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
To understand structural and thermodynamic features of disulfides within an α‐helix, a non‐redundant dataset comprising of 5025 polypeptide chains containing 2311 disulfides was examined. Thirty‐five examples were found of intrahelical disulfides involving a CXXC motif between the N‐Cap and third helical positions. GLY and PRO were the most common amino acids at positions 1 and 2, respectively. The N‐Cap residue for disulfide bonded CXXC motifs had average (ϕ,ψ) values of (−112 ± 25.2°, 106 ± 25.4°). To further explore conformational requirements for intrahelical disulfides, CYS pairs were introduced at positions N‐Cap‐3; 1,4; 7,10 in two helices of an Escherichia coli thioredoxin mutant lacking its active site disulfide (nSS Trx). In both helices, disulfides formed spontaneously during purification only at positions N‐Cap‐3. Mutant stabilities were characterized by chemical denaturation studies (in both oxidized and reduced states) and differential scanning calorimetry (oxidized state only). All oxidized as well as reduced mutants were destabilized relative to nSS Trx. All mutants were redox active, but showed decreased activity relative to wild‐type thioredoxin. Such engineered disulfides can be used to probe helix start sites in proteins of unknown structure and to introduce redox activity into proteins. Conversely, a protein with CYS residues at positions N‐Cap and 3 of an α‐helix is likely to have redox activity. Proteins 2010. © 2009 Wiley‐Liss, Inc.
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Affiliation(s)
- S Indu
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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19
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Khakshoor O, Nowick JS. Use of disulfide "staples" to stabilize beta-sheet quaternary structure. Org Lett 2009; 11:3000-3. [PMID: 19534505 DOI: 10.1021/ol901015a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Letter reports the use of disulfide linkages to stabilize a beta-sheet dimer with a well-defined structure in aqueous and dimethyl sulfoxide solutions. In this dimer, two cyclic beta-sheet peptides are connected by disulfide linkages at the non-hydrogen-bonded rings. The cyclic beta-sheet "domains" interact through hydrogen bonding to form a four-stranded beta-sheet structure. This interaction results in enhanced folding of the cyclic beta-sheet peptides.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, USA
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20
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Davidson DE, Hill BC. Stability of oxidized, reduced and copper bound forms of Bacillus subtilis Sco. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:275-81. [PMID: 19027886 DOI: 10.1016/j.bbapap.2008.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 10/21/2008] [Accepted: 10/24/2008] [Indexed: 11/30/2022]
Abstract
Sco is an accessory protein required for assembly of the Cu(A) center of cytochrome c oxidase. Functions proposed for Sco include as a copper chaperone and as a thiol-disulfide exchange protein. Differential scanning calorimetry (DSC) is used here to assess the interaction between the Bacillis subtilis version of Sco (BsSco) and Cu(II). When BsSco binds Cu(II) its melting temperature increases by 23 degrees C, which corresponds to an equilibrium dissociation constant of 3.50 pM. In contrast BsSco exhibits a much weaker affinity for Cu(I) (K(D)=10 microM). BsSco-Cu(II) is stable over days indicating an extremely slow dissociation for BsSco-Cu(II). However, at high ionic strength in the presence of excess copper, BsSco-Cu(II) returns to its oxidized, disulfide-bonded state and loses its copper binding capacity with a half time of 100 s. DSC of BsSco at high ionic strength indicates an increase in stability of metal free, reduced BsSco combined with a small destabilization of BsSco-Cu(II). It is proposed that BsSco undergoes an ionic strength induced conformational change that promotes electron transfer from the thiol groups on BsSco to Cu(II) to effect copper release. Such a redox transformation could be an important aspect of the copper transfer role proposed for BsSco in Cu(A) assembly.
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Affiliation(s)
- David E Davidson
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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21
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Sundaramoorthy E, Maiti S, Brahmachari SK, Sengupta S. Predicting protein homocysteinylation targets based on dihedral strain energy and pKa of cysteines. Proteins 2008; 71:1475-83. [PMID: 18076028 DOI: 10.1002/prot.21846] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A multitude of complex diseases have been linked to elevated homocysteine levels; however, till date there is no plausible explanation for a single amino acid's involvement in so many diseases. Since homocysteine is a reactive thiol amino acid and the majority of plasma homocysteine is protein thiol bound, we hypothesized that homocysteine might bind to accessible cysteine residues in target proteins, thereby modulating its structure or function or both. The parameters that dictate homocysteine-protein interaction are not well understood, and the few known homocysteine binding proteins were identified by a candidate protein approach. In this study, we identified potential homocysteine interacting proteins based on cysteine content, solvent accessibility of cysteine residues, and dihedral strain energies and pKa of these cysteines. Pathway mapping of the cysteine-rich proteins revealed that proteins in the coagulation cascade, notch receptor-mediated signaling, LDL endocytosis, programmed cell death, and extracellular matrix proteins were significantly over-represented with cysteine-rich proteins, and we believe that homocysteine has a high probability to bind to proteins in these pathways. In fact, several clinical studies have implicated high homocysteine levels to be associated with diseases like thrombosis, neural tube defects, and so forth, which result from dysfunction of one or more of the proteins identified in our study. Further, we successfully validated our prediction parameters on the proteins that have already been experimentally shown to bind homocysteine, and our structural analysis argues a plausible explanation for these prior reported protein interactions with homocysteine that could not be previously explained.
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Affiliation(s)
- Elayanambi Sundaramoorthy
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Delhi 110007, India
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22
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Dubey VK, Lee J, Somasundaram T, Blaber S, Blaber M. Spackling the crack: stabilizing human fibroblast growth factor-1 by targeting the N and C terminus beta-strand interactions. J Mol Biol 2007; 371:256-68. [PMID: 17570396 DOI: 10.1016/j.jmb.2007.05.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 04/22/2007] [Accepted: 05/21/2007] [Indexed: 10/23/2022]
Abstract
The beta-trefoil protein human fibroblast growth factor-1 (FGF-1) is made up of a six-stranded antiparallel beta-barrel closed off on one end by three beta-hairpins, thus exhibiting a 3-fold axis of structural symmetry. The N and C terminus beta-strands hydrogen bond to each other and their interaction is postulated from both NMR and X-ray structure data to be important in folding and stability. Specific mutations within the adjacent N and C terminus beta-strands of FGF-1 are shown to provide a substantial increase in stability. This increase is largely correlated with an increased folding rate constant, and with a smaller but significant decrease in the unfolding rate constant. A series of stabilizing mutations are subsequently combined and result in a doubling of the DeltaG value of unfolding. When taken in the context of previous studies of stabilizing mutations, the results indicate that although FGF-1 is known for generally poor thermal stability, the beta-trefoil architecture appears capable of substantial thermal stability. Targeting stabilizing mutations within the N and C terminus beta-strand interactions of a beta-barrel architecture may be a generally useful approach to increase protein stability. Such stabilized mutations of FGF-1 are shown to exhibit significant increases in effective mitogenic potency, and may prove useful as "second generation" forms of FGF-1 for application in angiogenic therapy.
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Affiliation(s)
- Vikash Kumar Dubey
- Department of Biomedical Sciences, Florida State University, Tallahassee FL 32306, USA
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Prajapati RS, Das M, Sreeramulu S, Sirajuddin M, Srinivasan S, Krishnamurthy V, Ranjani R, Ramakrishnan C, Varadarajan R. Thermodynamic effects of proline introduction on protein stability. Proteins 2007; 66:480-91. [PMID: 17034035 DOI: 10.1002/prot.21215] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The amino acid Pro is more rigid than other naturally occurring amino acids and, in proteins, lacks an amide hydrogen. To understand the structural and thermodynamic effects of Pro substitutions, it was introduced at 13 different positions in four different proteins, leucine-isoleucine-valine binding protein, maltose binding protein, ribose binding protein, and thioredoxin. Three of the maltose binding protein mutants were characterized by X-ray crystallography to confirm that no structural changes had occurred upon mutation. In the remaining cases, fluorescence and CD spectroscopy were used to show the absence of structural change. Stabilities of wild type and mutant proteins were characterized by chemical denaturation at neutral pH and by differential scanning calorimetry as a function of pH. The mutants did not show enhanced stability with respect to chemical denaturation at room temperature. However, 6 of the 13 single mutants showed a small but significant increase in the free energy of thermal unfolding in the range of 0.3-2.4 kcal/mol, 2 mutants showed no change, and 5 were destabilized. In five of the six cases, the stabilization was because of reduced entropy of unfolding. However, the magnitude of the reduction in entropy of unfolding was typically several fold larger than the theoretical estimate of -4 cal K(-1) mol(-1) derived from the relative areas in the Ramachandran map accessible to Pro and Ala residues, respectively. Two double mutants were constructed. In both cases, the effects of the single mutations on the free energy of thermal unfolding were nonadditive.
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Chakraborty K, Durani V, Miranda E, Citron M, Liang X, Schleif W, Joyce J, Varadarajan R. Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. Biochem J 2006; 399:483-91. [PMID: 16827663 PMCID: PMC1615908 DOI: 10.1042/bj20060588] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding cell-tropism of the virus. 447-52D is a monoclonal antibody that recognizes the conserved tip of the V3 loop in a beta-turn conformation. This antibody has previously been shown to neutralize diverse strains of the virus. In an attempt to generate an immunogen competent to generate 447-52D-like antibodies, the known epitope of 447-52D was inserted at three different surface loop locations in the small, stable protein Escherichia coli Trx (thioredoxin). At one of the three locations (between residues 74 and 75), the insertion was tolerated, the resulting protein was stable and soluble, and bound 447-52D with an affinity similar to that of intact gp120. Upon immunization, the V3 peptide-inserted Trx scaffold was able to generate anti-V3 antibodies that could compete out 447-52D binding to gp120. Epitope mapping studies demonstrated that these anti-V3 antibodies recognized the same epitope as 447-52D. Although the 447-52D-type antibodies were estimated to be present at concentrations of 50-400 microg/ml of serum, these were not able to effect neutralization of strains like JRFL and BAL but could neutralize the sensitive MN strain. The data suggest that because of the low accessibility of the V3 loop on primary isolates such as JRFL, it will be difficult to elicit a V3-specific, 447-52D-like antibody response to effectively neutralize such isolates.
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Affiliation(s)
- Kausik Chakraborty
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Venuka Durani
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | - Michael Citron
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
| | - Xiaoping Liang
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
| | | | - Joseph G. Joyce
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
- Correspondence may be addressed to either of the authors (email or )
| | - Raghavan Varadarajan
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
- ‡Chemical Biology Unit, Jawaharlal Center for Advanced Scientific Research, Jakkur, P.O., Bangalore 560 004, India
- Correspondence may be addressed to either of the authors (email or )
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