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Vaz DC, Rodrigues JR, Loureiro-Ferreira N, Müller TD, Sebald W, Redfield C, Brito RMM. Lessons on protein structure from interleukin-4: All disulfides are not created equal. Proteins 2024; 92:219-235. [PMID: 37814578 DOI: 10.1002/prot.26611] [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: 03/01/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023]
Abstract
Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.
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Affiliation(s)
- Daniela C Vaz
- School of Health Sciences, Polytechnic of Leiria, Leiria, Portugal
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | - J Rui Rodrigues
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | | | - Thomas D Müller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, Würzburg, Germany
| | - Walter Sebald
- Department of Physiological Chemistry II, Theodor-Boveri-Institute (Biocentre), University of Würzburg, Würzburg, Germany
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rui M M Brito
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
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2
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Chen J, Xu M, Wang L, Li T, Li Z, Wang T, Li P. Converting lysozyme to hydrogel: A multifunctional wound dressing that is more than antibacterial. Colloids Surf B Biointerfaces 2022; 219:112854. [PMID: 36154996 DOI: 10.1016/j.colsurfb.2022.112854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/27/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
Abstract
Wounds are usually irregular in shapes, and accompanied with a series of disorders such as hemorrhage and bacteria contamination. Here, we report a multifunctional hydrogel prepared by phase-transited lysozyme (PTL), which presents antimicrobial, injectable, self-healing, tissue adhesive, hemostatic and biodegradable properties that fit the requirements of wound treatment. The lysozyme was unfolded under the action of tris(2-carboxyethyl)phosphine (TCEP), and then self-assembled into a hydrogel (PTLG). The phase transition expanded the antibacterial spectrum of lysozyme, PTLG effectively killed both Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis) and Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii) on contact. This dynamically cross-linked hydrogel exhibited injectable and self-healing abilities, and was capable of adapting to various wound morphologies. The tissue-adhesive nature derived from phase-transition, endowed PTLG with hemostatic effect. Meanwhile, PTLG exhibited biocompatibility towards mammalian cells. Furthermore, its anti-infective ability in vivo was verified in a mouse subcutaneous infection model, more than 98 % of S. epidermidis was reduced under PTLG injection. And PTLG could be biodegraded within four weeks in mice body. Overall, the proposed PTLG is a promising multifunctional dressing material that could accommodate the various demands of complex and deep wounds.
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Affiliation(s)
- Jingjie Chen
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China
| | - Miao Xu
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China; Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Lei Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China
| | - Tian Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China
| | - Ziyue Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China; Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Tengjiao Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China; Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
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3
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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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4
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Renawala HK, Chandrababu KB, Topp EM. Fibrillation of Human Calcitonin and Its Analogs: Effects of Phosphorylation and Disulfide Reduction. Biophys J 2020; 120:86-100. [PMID: 33220304 DOI: 10.1016/j.bpj.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/24/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022] Open
Abstract
Some therapeutic peptides self-assemble in solution to form ordered, insoluble, β-sheet-rich amyloid fibrils. This physical instability can result in reduced potency, cause immunogenic side effects, and limit options for formulation. Understanding the mechanisms of fibrillation is key to developing rational mitigation strategies. Here, amide hydrogen-deuterium exchange with mass spectrometric analysis (HDX-MS) coupled with proteolytic digestion was used to identify the early stage interactions leading to fibrillation of human calcitonin (hCT), a peptide hormone important in calcium metabolism. hCT fibrillation kinetics was sigmoidal, with lag, growth, and plateau phases as shown by thioflavin T and turbidity measurements. HDX-MS of fibrillating hCT (pH 7.4; 25°C) suggested early involvement of the N-terminal (1-11) and central (12-19) fragments in interactions during the lag phase, whereas C-terminal fragments (20-32 and 26-32) showed limited involvement during this period. The residue-level information was used to develop phosphorylated hCT analogs that showed modified fibrillation that depended on phosphorylation site. Phosphorylation in the central region resulted in complete inhibition of fibrillation for the phospho-Thr-13 hCT analog, whereas phosphorylation in the N-terminal and C-terminal regions inhibited but did not prevent fibrillation. Reduction of the Cys1-Cys7 disulfide bond resulted in faster fibrillation with involvement of different hCT residues as indicated by pulsed HDX-MS. Together, the results demonstrate that small structural changes have significant effects on hCT fibrillation and that understanding these effects can inform the rational development of fibrillation-resistant hCT analogs.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Karthik B Chandrababu
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana; National Institute for Bioprocessing Research and Training, Dublin, Ireland.
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5
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Wang F, Diesendruck CE. Effect of disulphide loop length on mechanochemical structural stability of macromolecules. Chem Commun (Camb) 2020; 56:2143-2146. [DOI: 10.1039/c9cc07439b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Polymer chains folded with a single disulphide loop are shown to present distinct rates of mechanochemical fragmentation.
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Affiliation(s)
- Feng Wang
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Institute
- Technion – Israel Institute of Technology
- Haifa
- Israel
- School of Chemical Engineering
| | - Charles E. Diesendruck
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Institute
- Technion – Israel Institute of Technology
- Haifa
- Israel
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6
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Indrakumar S, Zalar M, Pohl C, Nørgaard A, Streicher W, Harris P, Golovanov AP, Peters GH. Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR. J Phys Chem B 2019; 123:4867-4877. [DOI: 10.1021/acs.jpcb.9b02370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Sowmya Indrakumar
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Matja Zalar
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Christin Pohl
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
- Novozymes, Krogshoejvej 36, Bagsvaerd 2880, Denmark
| | | | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Alexander P. Golovanov
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, U.K
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
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7
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R. S, J. J, A. TS. Purification, characterization, molecular modeling and docking study of fish waste protease. Int J Biol Macromol 2018; 118:569-583. [DOI: 10.1016/j.ijbiomac.2018.06.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 11/29/2022]
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8
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Denaturation and Aggregation of Interferon-τ in Aqueous Solution. Pharm Res 2018; 35:137. [DOI: 10.1007/s11095-018-2418-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/22/2018] [Indexed: 10/16/2022]
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9
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Rani A, Venkatesu P. Changing relations between proteins and osmolytes: a choice of nature. Phys Chem Chem Phys 2018; 20:20315-20333. [DOI: 10.1039/c8cp02949k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stabilization and destabilization of the protein in the presence of any additive is mainly attributed to its preferential exclusion from protein surface and its preferential binding to the protein surface, respectively.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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10
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Atamas N, Bardik V, Bannikova A, Grishina O, Lugovskoi E, Lavoryk S, Makogonenko Y, Korolovych V, Nerukh D, Paschenko V. The effect of water dynamics on conformation changes of albumin in pre-denaturation state: photon correlation spectroscopy and simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Lühmann T, Schmidt M, Leiske MN, Spieler V, Majdanski TC, Grube M, Hartlieb M, Nischang I, Schubert S, Schubert US, Meinel L. Site-Specific POxylation of Interleukin-4. ACS Biomater Sci Eng 2017; 3:304-312. [DOI: 10.1021/acsbiomaterials.6b00578] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tessa Lühmann
- Institute
of Pharmacy and Food Chemistry, University of Würzburg, Am
Hubland, DE-97074 Würzburg, Germany
| | - Marcel Schmidt
- Institute
of Pharmacy and Food Chemistry, University of Würzburg, Am
Hubland, DE-97074 Würzburg, Germany
| | - Meike N. Leiske
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Valerie Spieler
- Institute
of Pharmacy and Food Chemistry, University of Würzburg, Am
Hubland, DE-97074 Würzburg, Germany
| | - Tobias C. Majdanski
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Mandy Grube
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Matthias Hartlieb
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Ivo Nischang
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Stephanie Schubert
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
- Department
of Pharmaceutical Technology, Friedrich Schiller University Jena, Otto-Schott-Strasse 41, DE-07747 Jena, Germany
| | - Ulrich S. Schubert
- Institute of Organic and Macromolecular Chemistry [IOMC], Friedrich Schiller University Jena, Humboldtstrasse 10, DE-07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, DE-07743 Jena, Germany
| | - Lorenz Meinel
- Institute
of Pharmacy and Food Chemistry, University of Würzburg, Am
Hubland, DE-97074 Würzburg, Germany
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12
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Rani A, Jayaraj A, Jayaram B, Pannuru V. Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation. Sci Rep 2016; 6:23656. [PMID: 27025561 PMCID: PMC4812290 DOI: 10.1038/srep23656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress response. A number of models using these molecules are now poised to address a wide range of problems in biology. Here, a combination of biophysical measurements and molecular dynamics (MD) simulation method is used to examine the effect of trimethylamine-N-oxide (TMAO) on stem bromelain (BM) structure, stability and function. From the analysis of our results, we found that TMAO destabilizes BM hydrophobic pockets and active site as a result of concerted polar and non-polar interactions which is strongly evidenced by MD simulation carried out for 250 ns. This destabilization is enthalpically favourable at higher concentrations of TMAO while entropically unfavourable. However, to the best of our knowledge, the results constitute first detailed unambiguous proof of destabilizing effect of most commonly addressed TMAO on the interactions governing stability of BM and present plausible mechanism of protein unfolding by TMAO.
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Affiliation(s)
- Anjeeta Rani
- Department of Chemistry, University of Delhi, Delhi-110 007, India
| | - Abhilash Jayaraj
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology, New Delhi-110 016, India.,Supercomputing Facility for Bioinformatics &Computational Biology, Indian Institute of Technology, New Delhi-110 016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi-110 016, India
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13
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Haglund E. Engineering covalent loops in proteins can serve as an on/off switch to regulate threaded topologies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354107. [PMID: 26291088 DOI: 10.1088/0953-8984/27/35/354107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots in proteins are under active investigation motivating refinements of current techniques and the development of tools to better understand the knotted topology. A strong focus is to identify new knots and expand upon the current understanding of their complex topology. Previous work has shown that the knotted topology, even in the simplest case of knots, encompasses a variety of unique challenges in folding and tying a chain. To bypass many of the in vitro experimental complications involved in working with knots, it is useful to apply methodologies to a more simplified system. The pierced lasso bundles (PLB), we discovered where a single disulphide bridge holds the threaded topology together, presents a simpler system to study knots in vitro. Having a disulphide bridge as an on/off switch between the threaded/unthreaded topology is advantageous because a covalent loop allows manipulation of the knot without directly altering affecting secondary and tertiary structure. Because disulphide bridges are commonly used in protein engineering, a pierced lasso (PL) topology can be easily introduced into a protein of interest to form a knotted topology within a given secondary structure. It is also important to take into account that if formed, disulphides can inadvertently introduce an unwanted PL. This was found upon determination of the crystal structure (PDB code 2YHG) of the recently de novo designed nucleoside hydrolase. Our detailed investigations of the PL presented here will allow researchers to look at the introduction of disulphide bridges in a larger context with respect to potential geometrical consequences on the structure and functional properties of proteins.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California, San Diego (UCSD), La Jolla, CA 92093, USA. Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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14
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Borzova VA, Markossian KA, Kara DA, Kurganov B. Kinetic regime of dithiothreitol-induced aggregation of bovine serum albumin. Int J Biol Macromol 2015; 80:130-8. [PMID: 26116389 DOI: 10.1016/j.ijbiomac.2015.06.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/18/2015] [Accepted: 06/20/2015] [Indexed: 12/25/2022]
Abstract
A search for agents, which are capable of effectively suppressing protein aggregation, and elaboration of the appropriate test systems, are among important problems of modern biochemistry and biotechnology. One such test system is based on dithiothreitol (DTT)-induced aggregation of bovine serum albumin (BSA). Study of the kinetics of DTT-induced aggregation of BSA by asymmetric flow field flow fractionation showed that a decrease in the portion of the non-aggregated protein in time followed the exponential law, the rate constant of the first order remaining unchanged at varying protein concentration (0.1M Na-phosphate buffer, pH 7.0; 45 °C). The obtained results indicate that the rate-limiting stage of the general aggregation process is that of unfolding of the protein molecule. When studying the kinetics of DTT-induced aggregation of BSA by dynamic light scattering, we proposed to use parameter K(LS) as a measure of the initial rate of aggregation. Parameter K(LS) corresponds to the initial slope of the dependence of (I-I0)(0.5) on time (I0 and I are the initial and current values of the light scattering intensity, respectively). The K(LS) value has been applied to estimate anti-aggregation activity of chemical chaperones (arginine, its derivatives and proline).
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Affiliation(s)
- Vera A Borzova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Kira A Markossian
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Dmitriy A Kara
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Boris Kurganov
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia.
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15
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A theoretical study of the unfolding pathway of reduced Human serum albumin. J Mol Model 2015; 21:106. [DOI: 10.1007/s00894-015-2659-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/16/2015] [Indexed: 12/12/2022]
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16
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Rani A, Venkatesu P. Insights into the interactions between enzyme and co-solvents: Stability and activity of stem bromelain. Int J Biol Macromol 2015; 73:189-201. [DOI: 10.1016/j.ijbiomac.2014.10.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
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17
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Haglund E, Sulkowska JI, Noel JK, Lammert H, Onuchic JN, Jennings PA. Pierced Lasso Bundles are a new class of knot-like motifs. PLoS Comput Biol 2014; 10:e1003613. [PMID: 24945798 PMCID: PMC4063663 DOI: 10.1371/journal.pcbi.1003613] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/26/2014] [Indexed: 01/11/2023] Open
Abstract
A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California at San Diego (UCSD), La Jolla, California, United States of America
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | | | - Jeffrey K. Noel
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Heiko Lammert
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Patricia A. Jennings
- Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, California, United States of America
- * E-mail:
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18
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Salam NK, Adzhigirey M, Sherman W, Pearlman DA. Structure-based approach to the prediction of disulfide bonds in proteins. Protein Eng Des Sel 2014; 27:365-74. [PMID: 24817698 DOI: 10.1093/protein/gzu017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein engineering remains an area of growing importance in pharmaceutical and biotechnology research. Stabilization of a folded protein conformation is a frequent goal in projects that deal with affinity optimization, enzyme design, protein construct design, and reducing the size of functional proteins. Indeed, it can be desirable to assess and improve protein stability in order to avoid liabilities such as aggregation, degradation, and immunogenic response that may arise during development. One way to stabilize a protein is through the introduction of disulfide bonds. Here, we describe a method to predict pairs of protein residues that can be mutated to form a disulfide bond. We combine a physics-based approach that incorporates implicit solvent molecular mechanics with a knowledge-based approach. We first assign relative weights to the terms that comprise our scoring function using a genetic algorithm applied to a set of 75 wild-type structures that each contains a disulfide bond. The method is then tested on a separate set of 13 engineered proteins comprising 15 artificial stabilizing disulfides introduced via site-directed mutagenesis. We find that the native disulfide in the wild-type proteins is scored well, on average (within the top 6% of the reasonable pairs of residues that could form a disulfide bond) while 6 out of the 15 artificial stabilizing disulfides scored within the top 13% of ranked predictions. Overall, this suggests that the physics-based approach presented here can be useful for triaging possible pairs of mutations for disulfide bond formation to improve protein stability.
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Affiliation(s)
- Noeris K Salam
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Matvey Adzhigirey
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Woody Sherman
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - David A Pearlman
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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19
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Anoop A, Ranganathan S, Das Dhaked B, Jha NN, Pratihar S, Ghosh S, Sahay S, Kumar S, Das S, Kombrabail M, Agarwal K, Jacob RS, Singru P, Bhaumik P, Padinhateeri R, Kumar A, Maji SK. Elucidating the role of disulfide bond on amyloid formation and fibril reversibility of somatostatin-14: relevance to its storage and secretion. J Biol Chem 2014; 289:16884-903. [PMID: 24782311 DOI: 10.1074/jbc.m114.548354] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The storage of protein/peptide hormones within subcellular compartments and subsequent release are crucial for their native function, and hence these processes are intricately regulated in mammalian systems. Several peptide hormones were recently suggested to be stored as amyloids within endocrine secretory granules. This leads to an apparent paradox where storage requires formation of aggregates, and their function requires a supply of non-aggregated peptides on demand. The precise mechanism behind amyloid formation by these hormones and their subsequent release remain an open question. To address this, we examined aggregation and fibril reversibility of a cyclic peptide hormone somatostatin (SST)-14 using various techniques. After proving that SST gets stored as amyloid in vivo, we investigated the role of native structure in modulating its conformational dynamics and self-association by disrupting the disulfide bridge (Cys(3)-Cys(14)) in SST. Using two-dimensional NMR, we resolved the initial structure of somatostatin-14 leading to aggregation and further probed its conformational dynamics in silico. The perturbation in native structure (S-S cleavage) led to a significant increase in conformational flexibility and resulted in rapid amyloid formation. The fibrils formed by disulfide-reduced noncyclic SST possess greater resistance to denaturing conditions with decreased monomer releasing potency. MD simulations reveal marked differences in the intermolecular interactions in SST and noncyclic SST providing plausible explanation for differential aggregation and fibril reversibility observed experimentally in these structural variants. Our findings thus emphasize that subtle changes in the native structure of peptide hormone(s) could alter its conformational dynamics and amyloid formation, which might have significant implications on their reversible storage and secretion.
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Affiliation(s)
- Arunagiri Anoop
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Srivastav Ranganathan
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Bhagwan Das Dhaked
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Narendra Nath Jha
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Supriya Pratihar
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Saikat Ghosh
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Shruti Sahay
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Santosh Kumar
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Subhadeep Das
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, the IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | - Mamata Kombrabail
- the Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005
| | - Kumud Agarwal
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Reeba S Jacob
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Praful Singru
- the School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 751 005, and
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ranjith Padinhateeri
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076
| | - Ashutosh Kumar
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
| | - Samir K Maji
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076,
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20
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Castellanos MM, Colina CM. Molecular Dynamics Simulations of Human Serum Albumin and Role of Disulfide Bonds. J Phys Chem B 2013; 117:11895-905. [DOI: 10.1021/jp402994r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Maria Monica Castellanos
- Department of Materials Science
and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Coray M. Colina
- Department of Materials Science
and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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21
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The role of trehalose for metastable state and functional form of recombinant interferon beta-1b. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Paris G, Kraszewski S, Ramseyer C, Enescu M. About the structural role of disulfide bridges in serum albumins: evidence from protein simulated unfolding. Biopolymers 2012; 97:889-98. [PMID: 22899364 DOI: 10.1002/bip.22096] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues.
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Affiliation(s)
- Guillaume Paris
- Faculté des Sciences et Techniques, La Bouloie, Université de Franche-Comté, Besançon cedex, France
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23
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Haglund E, Sułkowska JI, He Z, Feng GS, Jennings PA, Onuchic JN. The unique cysteine knot regulates the pleotropic hormone leptin. PLoS One 2012; 7:e45654. [PMID: 23029163 PMCID: PMC3454405 DOI: 10.1371/journal.pone.0045654] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/20/2012] [Indexed: 11/30/2022] Open
Abstract
Leptin plays a key role in regulating energy intake/expenditure, metabolism and hypertension. It folds into a four-helix bundle that binds to the extracellular receptor to initiate signaling. Our work on leptin revealed a hidden complexity in the formation of a previously un-described, cysteine-knotted topology in leptin. We hypothesized that this unique topology could offer new mechanisms in regulating the protein activity. A combination of in silico simulation and in vitro experiments was used to probe the role of the knotted topology introduced by the disulphide-bridge on leptin folding and function. Our results surprisingly show that the free energy landscape is conserved between knotted and unknotted protein, however the additional complexity added by the knot formation is structurally important. Native state analyses led to the discovery that the disulphide-bond plays an important role in receptor binding and thus mediate biological activity by local motions on distal receptor-binding sites, far removed from the disulphide-bridge. Thus, the disulphide-bridge appears to function as a point of tension that allows dissipation of stress at a distance in leptin.
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Affiliation(s)
- Ellinor Haglund
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - Joanna I. Sułkowska
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - Zhao He
- Department of Pathology; School of Medicine and Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gen-Sheng Feng
- Department of Pathology; School of Medicine and Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Patricia A. Jennings
- Department of Chemistry and Biochemistry and Center for theoretical Biological Physics (CTBP), University of California San Diego, La Jolla, California, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological physics and Department of Physics and Astronomy, Chemistry, and Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
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24
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Duppatla V, Gjorgjevikj M, Schmitz W, Kottmair M, Mueller TD, Sebald W. Enzymatic deglutathionylation to generate interleukin-4 cysteine muteins with free thiol. Bioconjug Chem 2012; 23:1396-405. [PMID: 22681442 DOI: 10.1021/bc2004389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interleukin-4 (IL-4) is a prototypical regulator protein of the immune system that is crucial for the pathogenesis and maintenance of asthma and other atopic diseases. It, together with IL-13, uses the IL-4 receptor α chain (IL-4Rα) to signal into immune and other cells. An IL-4 mutein acting as a dual IL-4/IL-13 receptor antagonist is in clinical development. Here, it is described how IL-4 muteins containing a single engineered cysteine with a free thiol can be prepared and used for site-specific chemical modification. The muteins were initially expressed in E. coli, refolded, and purified, but not in a fully reduced nonconjugated form. Attempts to reduce the cysteine chemically failed because the native disulfide bonds of IL-4 were also reduced under similar conditions. Therefore, an enzymatic procedure was developed to reduce glutathionylated IL-4 cysteine muteins employing glutaredoxin and reduced glutathione. Cysteine muteins engineered at four different positions around the IL-4Rα binding site were enzymatically reduced at different rates. All muteins were prepared with free thiol in reasonable yield and were modified by N-ethylmaleimide (NEM) or maleimido-PEG. The effect on IL-4Rα binding of cysteine substitution and of the site-specific modification by glutathione, N-ethylmaleimide (NEM), or a branched 2.36 kDa poly(ethylene glycol) (PEG) will be discussed.
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Affiliation(s)
- Viswanadham Duppatla
- Lehrstuhl für Physiologische Chemie II, Theodor-Boveri-Institut für Biowissenschaften (Biozentrum) der Universität Würzburg, Würzburg, Germany.
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25
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Zhang L, Xu X, Luo Z, Zhang Y, Shen D, Peng L, Song J. Cu(ii)- and disulfide bonds-induced stabilization during the guanidine hydrochloride- and thermal-induced denaturation of NAD-glycohydrolase from the venom of Agkistrodon acutus. Metallomics 2011; 4:166-73. [PMID: 22045055 DOI: 10.1039/c1mt00135c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
NAD-glycohydrolase (AA-NADase) from Agkistrodon acutus venom is a unique multicatalytic enzyme with both NADase and AT(D)Pase-like activities. Among all identified NADases, only AA-NADase is a disulfide-linked dimer and contains Cu(2+). Cu(2+) and disulfide bonds are essential for its multicatalytic activity. In this study, the effects of Cu(2+) and disulfide-bonds on guanidine hydrochloride (GdnHCl)- and thermal-induced unfolding of AA-NADase have been investigated by fluorescence, circular dichroism (CD) and differential scanning calorimetry (DSC). Cu(2+) and disulfide bonds not only increase the free energy change during the GdnHCl-induced unfolding as determined by fluorescence, but also increase the overall enthalpy change and the transition temperature during the thermal-induced unfolding as determined by CD and DSC. The slope of the GdnHCl-induced unfolding curve at its midpoint and the heat capacity of thermal-induced unfolding are slightly affected by Cu(2+) but significantly decrease after reduction of three disulfide-bonds. This work suggests that Cu(2+) stabilizes the folded state by increasing the enthalpy of unfolding, while disulfide-bonds stabilize the folded state by increasing the enthalpy of unfolding and stabilizing the packing of hydrophobic residues. Thus both Cu(2+) and disulfide bonds play a structural role in its multicatalytic activity.
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Affiliation(s)
- Liyun Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
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26
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Wallner M, Hauser M, Himly M, Zaborsky N, Mutschlechner S, Harrer A, Asam C, Pichler U, van Ree R, Briza P, Thalhamer J, Bohle B, Achatz G, Ferreira F. Reshaping the Bet v 1 fold modulates T(H) polarization. J Allergy Clin Immunol 2011; 127:1571-8.e9. [PMID: 21420160 DOI: 10.1016/j.jaci.2011.01.064] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/28/2010] [Accepted: 01/31/2011] [Indexed: 11/27/2022]
Abstract
BACKGROUND Several alternative mechanisms have been proposed to explain why some proteins are able to induce a T(H)2-biased and IgE-mediated immune response. These include specific interactions with receptors of the innate immune system, proteolytic activities, allergen-associated carbohydrate structures, and intrinsic structural determinants. OBJECTIVES Available data suggest that a fold-dependent allergy-promoting mechanism could be a driving force for the T(H)2-polarization activity of Bet v 1, the major birch pollen allergen. METHODS Computer-aided sequence and fold analysis of the Bet v 1 family identified a short stretch susceptible for mutations inducing an altered fold of the entire molecule. With this knowledge, 7 consecutive amino acids of Bet v 1 were replaced with the homologous Mal d 1 sequence, creating the derivative BM4. RESULTS The minimal changes of the sequence led to a loss of the Bet v 1-like fold and influenced the immunologic behavior. Compared to wild-type Bet v 1, BM4 induced elevated T-cell proliferation of human PBMCs. In the mouse model, immunization with Bet v 1 absorbed to aluminum hydroxide triggered strong T(H)2 polarization, whereas BM4 immunization additionally recruited T(H)1 cells. Furthermore, the fold variant BM4 showed enhanced uptake by dendritic cells and a decreased susceptibility to endo-/lysosomal proteolysis. CONCLUSION Modifications in the 3-dimensional structure of Bet v 1.0101 resulted in a change of its immunologic properties. We observed that the fold alteration led to a modified crosstalk with dendritic cells and a shift of the immune response polarization toward a mixed T(H)1/T(H)2 cytokine production.
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Affiliation(s)
- Michael Wallner
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, Department of Molecular Biology, University of Salzburg, Salzburg, Austria.
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27
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Shen D, Xu X, Wu H, Peng L, Zhang Y, Song J, Su Q. Metal ion binding to anticoagulation factor II from the venom of Agkistrodon acutus: stabilization of the structure and regulation of the binding affinity to activated coagulation factor X. J Biol Inorg Chem 2011; 16:523-37. [PMID: 21197556 DOI: 10.1007/s00775-010-0752-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 12/14/2010] [Indexed: 11/26/2022]
Abstract
Anticoagulation factor II (ACF II) isolated from the venom of Agkistrodon acutus is an activated coagulation factor X (FXa)-binding protein with both anticoagulant and hypotensive activities. The thermodynamics of the binding of alkaline earth metal ions to ACF II and their effects on the stability of ACF II and the binding of ACF II to FXa were investigated by isothermal titration calorimetry, fluorescence, differential scanning calorimetry, and surface plasmon resonance. The binding of ACF II to FXa does not have an absolute requirement for Ca(2+). Mg(2+), Sr(2+), and Ba(2+) can induce the binding of ACF II to FXa. The radii of the cations bound in ACF II crucially affect the binding affinity of ACF II for cations and the structural stability of ACF II against guanidine hydrochloride and thermal denaturation, whereas the radii of cations bound in FXa markedly affect the binding affinity between ACF II and FXa. The binding affinities of ACF II for cations and the capacities of metal-induced stabilization of ACF II follow the same trend: Ca(2+) > Sr(2+) > Ba(2+). The metal-induced binding affinities of ACF II for FXa follow the trend Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). Although Mg(2+) shows significantly low binding affinity with ACF II, Mg(2+) is the most effective to induce the binding of ACF II with FXa. Our observations suggest that in blood the bindings of Ca(2+) in two sites of ACF II increase the structural stability of ACF II, but these bindings are not essential for the binding of ACF II with FXa, and that the binding of Mg(2+) and Ca(2+) to FXa may be essential for the recognition between FXa and ACF II. Like Ca(2+), the abundant Mg(2+) in blood also plays an important role in the anticoagulation of ACF II.
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Affiliation(s)
- Dengke Shen
- Department of Chemistry, University of Science and Technology of China, Hefei, People's Republic of China
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28
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Gadermaier G, Jahn-Schmid B, Vogel L, Egger M, Himly M, Briza P, Ebner C, Vieths S, Bohle B, Ferreira F. Targeting the cysteine-stabilized fold of Art v 1 for immunotherapy of Artemisia pollen allergy. Mol Immunol 2010; 47:1292-8. [DOI: 10.1016/j.molimm.2009.11.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 11/22/2009] [Accepted: 11/24/2009] [Indexed: 10/20/2022]
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29
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David C, Enescu M. Free Energy Calculations on Disulfide Bridges Reduction in Proteins by Combining ab Initio and Molecular Mechanics Methods. J Phys Chem B 2010; 114:3020-7. [DOI: 10.1021/jp910340t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catalina David
- Laboratoire de Chimie Physique et Rayonnement, UMR CEA E4, University of Franche-Comte, 16 route de Gray, 25030 Besancon, France
| | - Mironel Enescu
- Laboratoire de Chimie Physique et Rayonnement, UMR CEA E4, University of Franche-Comte, 16 route de Gray, 25030 Besancon, France
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30
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Wallner M, Himly M, Neubauer A, Erler A, Hauser M, Asam C, Mutschlechner S, Ebner C, Briza P, Ferreira F. The influence of recombinant production on the immunologic behavior of birch pollen isoallergens. PLoS One 2009; 4:e8457. [PMID: 20041109 PMCID: PMC2795169 DOI: 10.1371/journal.pone.0008457] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 12/01/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Allergic reactions towards the birch major pollen allergen Bet v 1 are among the most common causes of spring pollinosis in the temperate climate zone of the Northern hemisphere. Natural Bet v 1 is composed of a complex mixture of different isoforms. Detailed analysis of recombinant Bet v 1 isoforms revealed striking differences in immunologic as well as allergenic properties of the molecules, leading to a classification of Bet v 1 isoforms into high, medium, and low IgE binding proteins. Especially low IgE binding Bet v 1 isoforms have been described as ideal candidates for desensitizing allergic patients with allergen specific immunotherapy (SIT). Since diagnosis and therapy of allergic diseases are highly dependent on recombinant proteins, continuous improvement of protein production is an absolute necessity. METHODOLOGY Therefore, two different methods for recombinant production of a low IgE binding Bet v 1 isoform were applied; one based on published protocols, the other by implementing latest innovations in protein production. Both batches of Bet v 1.0401 were extensively characterized by an array of physicochemical as well as immunological methods to compare protein primary structure, purity, quantity, folding, aggregation state, thermal stability, and antibody binding capacity. CONCLUSION The experiments demonstrated that IgE antibody binding properties of recombinant isoallergens can be significantly influenced by the production method directly affecting possible clinical applications of the molecules.
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Affiliation(s)
- Michael Wallner
- Christian Doppler Laboratory for Allergy Diagnosis and Therapy, University of Salzburg, Salzburg, Austria.
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31
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Arolas JL, Castillo V, Bronsoms S, Aviles FX, Ventura S. Designing Out Disulfide Bonds of Leech Carboxypeptidase Inhibitor: Implications for Its Folding, Stability and Function. J Mol Biol 2009; 392:529-46. [DOI: 10.1016/j.jmb.2009.06.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 05/04/2009] [Accepted: 06/18/2009] [Indexed: 11/26/2022]
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32
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Starikov EB, Nordén B. Physical rationale behind the nonlinear enthalpy-entropy compensation in DNA duplex stability. J Phys Chem B 2009; 113:4698-707. [PMID: 19278234 DOI: 10.1021/jp8089424] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical-chemical sense of nonlinear entropy-enthalpy compensation based upon the standard thermodynamical parameters of high-temperature melting for doublet units in DNA duplexes has been considered. We are able to show that there are three, with no other constraints equally plausible, principal levels of DNA melting/hybridization description. First, DNA structure assembly/disassembly can be seen from the viewpoint of the conventional equilibrium thermodynamics without taking special care of the heat capacity DeltaC(p) value (by simply setting it equal to zero). Second, it is possible to assume that the DeltaC(p) is finite, but independent of temperature. At this approximation level the high-temperature DNA melting cannot be described, but only some special transition between metastable states of DNA duplexes in water solutions in the vicinity of ice melting point. Third, both the latter transition and the high-temperature DNA melting can be reproduced by one and the same approach, if the DeltaC(p) is assumed to be temperature dependent. These three approximation levels are equally justified from the nonlinear entropy-enthalpy compensation standpoint and by a generalized theory of temperature effects on themodynamical stability as is outlined here. Applicability of each of the approximation levels involved is discussed.
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Affiliation(s)
- E B Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany.
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Ghanem M, Zhadin N, Callender R, Schramm VL. Loop-tryptophan human purine nucleoside phosphorylase reveals submillisecond protein dynamics. Biochemistry 2009; 48:3658-68. [PMID: 19191546 DOI: 10.1021/bi802339c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human PNP is a homotrimer containing three tryptophan residues at positions 16, 94, and 178, all remote from the catalytic site. The catalytic sites of PNP are located near the subunit-subunit interfaces where F159 is a catalytic site residue donated from an adjacent subunit. F159 covers the top (beta) surface of the ribosyl group at the catalytic site. QM/MM calculations of human PNP have shown that F159 is the center of the most mobile region of the protein providing access to the substrate in the active site. F159 is also the key residue in a cluster of hydrophobic residues that shield catalytic site ligands from bulk solvent. Trp-free human PNP (Leuko-PNP) was previously engineered by replacing the three Trp residues of native PNP with Tyr. From this active construct, a single Trp residue was placed in the catalytic site loop (F159W-Leuko-PNP) as a reporter group for the ribosyl region of the catalytic site. The F159W-Leuko-PNP fluorescence is red shifted compared to native PNP, suggesting a solvent-exposed Trp residue. Upon ligand binding (hypoxanthine), the 3-fold fluorescence quench confirms conformational packing of the catalytic site pocket hydrophobic cluster. F159W-Leuko-PNP has an on-enzyme thermodynamic equilibrium constant (Keq) near unity in the temperature range between 20 and 30 degrees C and nonzero enthalpic components, making it suitable for laser-induced T-jump analyses. T-jump relaxation kinetics of F159W-Leuko-PNP in equilibrium with substrates and/or products indicate the conformational equilibria of at least two ternary complex intermediates in the nano- to millisecond time scale (1000-10000 s-1) that equilibrate prior to the slower chemical step (approximately 200 s-1). F159W-Leuko-PNP provides a novel protein platform to investigate the protein conformational dynamics occurring prior to transition state formation.
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Affiliation(s)
- Mahmoud Ghanem
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Yuan Z, Wang R, Lee Y, Chen CY, Yu X, Wu Z, Huang D, Shen L, Chen ZW. Tuberculosis-induced variant IL-4 mRNA encodes a cytokine functioning as growth factor for (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate-specific Vgamma2Vdelta2 T cells. THE JOURNAL OF IMMUNOLOGY 2009; 182:811-9. [PMID: 19124724 DOI: 10.4049/jimmunol.182.2.811] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The possibility that mycobacterial infections induce variant cytokine mRNA encoding a functionally distinct protein for immune regulation has not been addressed. In this study, we reported that Mycobacterium tuberculosis and bacillus Calmette-Guérin infections of macaques induced expression of variant IL-4 (VIL-4) mRNA encoding a protein comprised of N-terminal 97 aa identical with IL-4, and unique C-terminal 96 aa including a signaling-related proline-rich motif. While VIL-4 could be stably produced as intact protein, the purified VIL-4 induced apparent expansion of phosphoantigen (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP)-specific Vgamma2Vdelta2 T cells in dose- and time-dependent manners. The unique C-terminal 96 aa bearing the proline-rich motif (PPPCPP) of VIL-4 appeared to confer the ability to expand Vgamma2Vdelta2 T cells, since simultaneously produced IL-4 had only a subtle effect on these gammadelta T cells. Moreover, VIL-4 seemed to use IL-4R alpha for signaling and activation, as the VIL-4-induced expansion of Vgamma2Vdelta2 T cells was blocked by anti-IL-4R alpha mAb but not anti-IL-4 mAb. Surprisingly, VIL-4-expanded Vgamma2Vdelta2 T cells after HMBPP stimulation appeared to be heterologous effector cells capable of producing IL-4, IFN-gamma, and TNF-alpha. Thus, mycobacterial infections of macaques induced variant mRNA encoding VIL-4 that functions as growth factor promoting expansion of HMBPP-specific Vgamma2Vdelta2 T effector cells.
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Affiliation(s)
- ZhuQing Yuan
- Department of Microbiology and Immunology, Center for Primate Biomedical Research, University of Illinois College of Medicine, Chicago, IL 60612, USA
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35
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David C, Foley S, Enescu M. Protein S–S bridge reduction: a Raman and computational study of lysozyme interaction with TCEP. Phys Chem Chem Phys 2009; 11:2532-42. [DOI: 10.1039/b815492a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Nikitina J, Shutova T, Melnik B, Chernyshov S, Marchenkov V, Semisotnov G, Klimov V, Samuelsson G. Importance of a single disulfide bond for the PsbO protein of photosystem II: protein structure stability and soluble overexpression in Escherichia coli. PHOTOSYNTHESIS RESEARCH 2008; 98:391-403. [PMID: 18709441 DOI: 10.1007/s11120-008-9327-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 07/01/2008] [Indexed: 05/09/2023]
Abstract
PsbO protein is an important constituent of the water-oxidizing complex, located on the lumenal side of photosystem II. We report here the efficient expression of the spinach PsbO in E. coli where the solubility depends entirely on the formation of the disulfide bond. The PsbO protein purified from a pET32 system that includes thioredoxin fusion is properly folded and functionally active. Urea unfolding experiments imply that the reduction of the single disulfide bridge decreases stability of the protein. Analysis of inter-residue contact density through the PsbO molecule shows that Cys51 is located in a cluster with high contact density. Reduction of the Cys28-Cys51 bond is proposed to perturb the packing interactions in this cluster and destabilize the protein as a whole. Taken together, our results give evidence that PsbO exists in solution as a compact highly ordered structure, provided that the disulfide bridge is not reduced.
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Affiliation(s)
- Julia Nikitina
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umea, Sweden
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37
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David C, Foley S, Mavon C, Enescu M. Reductive unfolding of serum albumins uncovered by Raman spectroscopy. Biopolymers 2008; 89:623-34. [PMID: 18322931 DOI: 10.1002/bip.20972] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The reductive unfolding of bovine serum albumin (BSA) and human serum albumin (HSA) induced by dithiothreitol (DTT) is investigated using Raman spectroscopy. The resolution of the S-S Raman band into both protein and oxidized DTT contributions provides a reliable basis for directly monitoring the S-S bridge exchange reaction. The related changes in the protein secondary structure are identified by analyzing the protein amide I Raman band. For the reduction of one S-S bridge of BSA, a mean Gibbs free energy of -7 kJ mol(-1) is derived by studying the reaction equilibrium. The corresponding value for the HSA S-S bridge reduction is -2 kJ mol(-1). The reaction kinetics observed via the S-S or amide I Raman bands are identical giving a reaction rate constant of (1.02 +/- 0.11) M(-1) s(-1) for BSA. The contribution of the conformational Gibbs free energy to the overall Gibbs free energy of reaction is further estimated by combining experimental data with ab initio calculations.
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Affiliation(s)
- Catalina David
- University of Franche-Comte, Laboratoire de Physico-Chimie et Rayonnement-Alain Chambaudet, UMR EA E4, 16 route de Gray, 25030 Besancon, France
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38
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Edgcomb SP, Aschrafi A, Kompfner E, Williamson JR, Gerace L, Hennig M. Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes. Protein Sci 2008; 17:420-30. [PMID: 18218716 DOI: 10.1110/ps.073246608] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The translation of the unspliced and partially spliced viral mRNAs that encode the late, structural proteins of HIV-1 depends on the viral-protein Rev. Oligomeric binding of Rev to the Rev response element (RRE) in these mRNAs promotes their export from the nucleus and thus controls their expression. Here, we compared the effects of hydrophobic to hydrophilic mutations within the oligomerization domain of Rev using assays for oligomeric RNA binding, protein structure, and export from the nucleus. Oligomeric RNA binding alone does not correlate well with RNA transport activity in the subset of mutants. However, protein structure as judged by CD spectroscopy does correlate well with Rev function. The oligomeric assembly of Rev-L18T is impaired but exhibits minor defects in structure and retains a basal level of activity in vivo. The prevalence of L18T in infected individuals suggests a positive selection mechanism for L18T modulation of Rev activity that may delay the onset of AIDS.
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Affiliation(s)
- Stephen P Edgcomb
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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39
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López de la Osa J, Bateman DA, Ho S, González C, Chakrabartty A, Laurents DV. Getting specificity from simplicity in putative proteins from the prebiotic earth. Proc Natl Acad Sci U S A 2007; 104:14941-6. [PMID: 17855563 PMCID: PMC1986592 DOI: 10.1073/pnas.0706876104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Indexed: 11/18/2022] Open
Abstract
Can unique protein structures arise from a limited set of amino acids present on the prebiotic earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited "alphabet" of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic earth.
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Affiliation(s)
- Jaime López de la Osa
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - David A. Bateman
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Sylvia Ho
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Carlos González
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - Avijit Chakrabartty
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Douglas V. Laurents
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
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Stirpe A, Sportelli L, Guzzi R. A comparative investigation of the thermal unfolding of pseudoazurin in the Cu(II)-holo and apo form. Biopolymers 2007; 83:487-97. [PMID: 16881076 DOI: 10.1002/bip.20579] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The contribution of the copper ion to the stability and to the unfolding pathway of pseudoazurin was investigated by a comparative analysis of the thermal unfolding of the Cu(II)-holo and apo form of the protein. The unfolding has been followed by calorimetry, fluorescence, optical density, and electron paramagnetic resonance (EPR) spectroscopy. The thermal transition of Cu(II)-holo pseudoazurin is irreversible and occurs between 60.0 and 67.3 degrees C, depending on the scan rate and technique used. The denaturation pathway of Cu(II)-holo pseudoazurin can be described by the Lumry-Eyring model: N --> U --> [corrected] F; the protein reversibly goes from the native (N) to the unfolded (U) state, and then irreversibly to the final (F) state. The simulation of the experimental calorimetric profiles, according to this model, allowed us to determine the thermodynamic and kinetic parameters of the two steps. The DeltaG value calculated for the Cu(II)-holo pseudoazurin is 39.2 kJ.mol(-1) at 25 degrees C. The sequence of events in the denaturation process of Cu(II)-holo pseudoazurin emergence starts with the disruption of the copper site and the hydrophobic core destabilization followed by the global protein unfolding. According to the EPR findings, the native type-1 copper ion shows type-2 copper features after the denaturation. The removal of the copper ion (apo form) significantly reduces the stability of the protein as evidenced by a DeltaG value of 16.5 kJ.mol(-1) at 25 degrees C. Moreover, the apo Paz unfolding occurs at 41.8 degrees C and is compatible with a two-state reversible process N --> [corrected] U.
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Affiliation(s)
- Andrea Stirpe
- Dipartimento di Fisica e Unità CNISM, Laboratorio di Biofisica Molecolare, Università della Calabria, Ponte P. Bucci - Cubo 30C, I-87036, Arcavacata di Rende (CS), Italy
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41
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Feige MJ, Hagn F, Esser J, Kessler H, Buchner J. Influence of the Internal Disulfide Bridge on the Folding Pathway of the CL Antibody Domain. J Mol Biol 2007; 365:1232-44. [PMID: 17112539 DOI: 10.1016/j.jmb.2006.10.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 08/25/2006] [Accepted: 10/16/2006] [Indexed: 11/26/2022]
Abstract
Disulfide bridges are one of the most important factors stabilizing the native structure of a protein. Whereas the basis for their stabilizing effect is well understood, their role in a protein folding reaction still seems to require further attention. We used the constant domain of the antibody light chain (C(L)), a representative of the ubiquitous immunoglobulin (Ig)-superfamily, to delineate the kinetic role of its single buried disulfide bridge. Independent of its redox state, the monomeric C(L) domain adopts a typical Ig-fold under native conditions and does not retain significant structural elements when unfolded. Interestingly, its folding pathway is strongly influenced by the disulfide bridge. The more stable oxidized protein folds via a highly structured on-pathway intermediate, whereas the destabilized reduced protein populates a misfolded off-pathway species on its way to the native state. In both cases, the formation of the intermediate species is shown to be independent of the isomerization state of the Tyr(141)-Pro(142) bond. Our results demonstrate that the internal disulfide bridge in an antibody domain restricts the folding pathway by bringing residues of the folding nucleus into proximity thus facilitating the way to the native state.
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Affiliation(s)
- Matthias J Feige
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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