1
|
Wang R, Liu M, Wang H, Xia J, Li H. GB Tags: Small Covalent Peptide Tags Based on Protein Fragment Reconstitution. Bioconjug Chem 2021; 32:1926-1934. [PMID: 34329559 DOI: 10.1021/acs.bioconjchem.1c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing peptide tags that can bind target proteins covalently under mild conditions is of great importance for a myriad of applications, ranging from chemical biology to biotechnology. Here we report the development of a small covalent peptide tag system, termed as GB tags, that can covalently label the target protein with high specificity and high yield under oxidizing conditions. The GB tags consist of a pair of short peptides, GN and GC (GN contains 45 residues and GC contains 19 residues). GN and GC, which are split from a parent protein GB1, can undergo protein fragment reconstitution to reconstitute the folded structure of the parent protein spontaneously. The engineered cysteines in GN and GC can readily form a disulfide bond oxidized by air oxygen after protein reconstitution. Using thermally stable variants of GB1, we identified two pairs of GB tags that display improved thermodynamic stability and binding affinity. They can serve as efficient covalent peptide tags for various applications, including specific labeling of mammalian cell surface receptors. We anticipate that these new GB tags will find applications in biochemical labeling as well as biomaterials, such as protein hydrogels.
Collapse
Affiliation(s)
- Ruidi Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada.,State Key Laboratory of Supramolecular Structure and Materials College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Miao Liu
- Department of Chemistry, Chinese University of Hong Kong, Hong Kong SRC, P. R. China
| | - Han Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Jiang Xia
- Department of Chemistry, Chinese University of Hong Kong, Hong Kong SRC, P. R. China
| | - Hongbin Li
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| |
Collapse
|
2
|
Wang R, Li J, Li X, Guo J, Liu J, Li H. Engineering protein polymers of ultrahigh molecular weight via supramolecular polymerization: towards mimicking the giant muscle protein titin. Chem Sci 2019; 10:9277-9284. [PMID: 32055313 PMCID: PMC7003960 DOI: 10.1039/c9sc02128k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/19/2019] [Indexed: 01/02/2023] Open
Abstract
Utilizing protein fragment reconstitution of a small protein GB1, we developed an efficient, supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight that mimic the giant muscle protein titin.
The giant muscle protein titin is the largest protein in cells and responsible for the passive elasticity of muscles. Titin, made of hundreds of individually folded globular domains, is a protein polymer with folded globular domains as its macromonomers. Due to titin's ultrahigh molecular weight, it has been challenging to engineer high molecular weight artificial protein polymers that mimic titin. Taking advantage of protein fragment reconstitution (PFR) of a small protein GB1, which can be reconstituted from its two split fragments GN and GC, here we report the development of an efficient, PFR-based supramolecular polymerization strategy to engineer protein polymers with ultrahigh molecular weight. We found that the engineered bifunctional protein macromonomers (GC-macromonomer-GN) can undergo supramolecular polymerization, in a way similar to condensation polymerization, via the reconstitution of GN and GC to produce protein polymers with ultrahigh molecular weight (with an average molecular weight of 0.5 MDa). Such high molecular weight linear protein polymers closely mimic titin and provide protein polymer building blocks for the construction of biomaterials with improved physical and mechanical properties.
Collapse
Affiliation(s)
- Ruidi Wang
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China.,Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Jiayu Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Xiumei Li
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China
| | - Jin Guo
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials , College of Chemistry , Jilin University , Changchun 130012 , P. R. China
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC V6T 1Z1 , Canada .
| |
Collapse
|
3
|
Wang R, Fu L, Liu J, Li H. Decorating protein hydrogels reversibly enables dynamic presentation and release of functional protein ligands on protein hydrogels. Chem Commun (Camb) 2019; 55:12703-12706. [DOI: 10.1039/c9cc06374a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilizing protein fragment reconstitution, we demonstrate the reversible and repeatable functionalization of protein hydrogels.
Collapse
Affiliation(s)
- Ruidi Wang
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
- State Key Laboratory of Supramolecular Structure and Materials
| | - Linglan Fu
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- P. R. China
| | - Hongbin Li
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| |
Collapse
|
4
|
Andersson H, Danelius E, Jarvoll P, Niebling S, Hughes AJ, Westenhoff S, Brath U, Erdélyi M. Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar β-Hairpins. ACS OMEGA 2017; 2:508-516. [PMID: 28261689 PMCID: PMC5331454 DOI: 10.1021/acsomega.6b00484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
We have evaluated the ability of nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies to describe the difference in the folding propensities of two structurally highly similar cyclic β-hairpins, comparing the outcome to that of molecular dynamics simulations. NAMFIS-type NMR ensemble analysis and CD spectroscopy were observed to accurately describe the consequence of altering a single interaction site, whereas a single-site 13C NMR chemical shift melting curve-based technique was not.
Collapse
Affiliation(s)
- Hanna Andersson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Emma Danelius
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Patrik Jarvoll
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Stephan Niebling
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Ashley J. Hughes
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Ulrika Brath
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Máté Erdélyi
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
- The
Swedish NMR Centre, Medicinaregatan
5c, SE-413 96 Gothenburg, Sweden
- E-mail: (M.E.)
| |
Collapse
|
5
|
Yageta S, Shibuya R, Imamura H, Honda S. Conformational and Colloidal Stabilities of Human Immunoglobulin G Fc and Its Cyclized Variant: Independent and Compensatory Participation of Domains in Aggregation of Multidomain Proteins. Mol Pharm 2017; 14:699-711. [DOI: 10.1021/acs.molpharmaceut.6b00983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seiki Yageta
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Risa Shibuya
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hiroshi Imamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Department of Computational
Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, AIST Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| |
Collapse
|
6
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
7
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
8
|
Li H, Kong N, Laver B, Liu J. Hydrogels Constructed from Engineered Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:973-987. [PMID: 26707834 DOI: 10.1002/smll.201502429] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/23/2015] [Indexed: 06/05/2023]
Abstract
Due to their various potential biomedical applications, hydrogels based on engineered proteins have attracted considerable interest. Benefitting from significant progress in recombinant DNA technology and protein engineering/design techniques, the field of protein hydrogels has made amazing progress. The latest progress of hydrogels constructed from engineered recombinant proteins are presented, mainly focused on biorecognition-driven physical hydrogels as well as chemically crosslinked hydrogels. The various bio-recognition based physical crosslinking strategies are discussed, as well as chemical crosslinking chemistries used to engineer protein hydrogels, and protein hydrogels' various biomedical applications. The future perspectives of this fast evolving field of biomaterials are also discussed.
Collapse
Affiliation(s)
- Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Na Kong
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Bryce Laver
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Junqiu Liu
- Key Lab for Supramolecular Structure and Materials, Jilin University, Changchun, Jilin Province, 130012, P. R. China
| |
Collapse
|
9
|
Abstract
Circular dichroism (CD) spectroscopy is a useful technique for studying protein-protein interactions in solution. CD in the far ultraviolet region (178-260 nm) arises from the amides of the protein backbone and is sensitive to the conformation of the protein. Thus, CD can determine whether there are changes in the conformation of proteins when they interact. Changes in the conformation of the protein complexes as a function of temperature or added denaturants, compared to the individual proteins, can be used to determine binding constants. CD bands in the near ultraviolet (350-260 nm) and visible regions arise from aromatic amino acid side chains and prosthetic groups. There are often changes in these regions when proteins bind to each other. Because CD is a quantitative technique, these changes are directly proportional to the amount of the protein-protein complexes formed and thus also can be used to estimate binding constants.
Collapse
Affiliation(s)
- Norma J Greenfield
- Associate Professor (retired), Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane West, Piscataway, NJ, 08854-8021, USA,
| |
Collapse
|
10
|
Vorov OK, Livesay DR, Jacobs DJ. Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Biophys J 2011; 100:1129-38. [PMID: 21320459 DOI: 10.1016/j.bpj.2011.01.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 01/07/2011] [Indexed: 11/15/2022] Open
Abstract
Previously, we employed a Maxwell counting distance constraint model (McDCM) to describe α-helix formation in polypeptides. Unlike classical helix-coil transition theories, the folding mechanism derives from nonadditivity in conformational entropy caused by rigidification of molecular structure as intramolecular cross-linking interactions form along the backbone. For example, when a hydrogen bond forms within a flexible region, both energy and conformational entropy decrease. However, no conformational entropy is lost when the region is already rigid because atomic motions are not constrained further. Unlike classical zipper models, the same mechanism also describes a coil-to-β-hairpin transition. Special topological features of the helix and hairpin structures allow the McDCM to be solved exactly. Taking full advantage of the fact that Maxwell constraint counting is a mean field approximation applied to the distribution of cross-linking interactions, we present an exact transfer matrix method that does not require any special topological feature. Upon application of the model to proteins, cooperativity within the folding transition is yet again appropriately described. Notwithstanding other contributing factors such as the hydrophobic effect, this simple model identifies a universal mechanism for cooperativity within polypeptide and protein-folding transitions, and it elucidates scaling laws describing hydrogen-bond patterns observed in secondary structure. In particular, the native state should have roughly twice as many constraints as there are degrees of freedom in the coil state to ensure high fidelity in two-state folding cooperativity, which is empirically observed.
Collapse
Affiliation(s)
- Oleg K Vorov
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | | | | |
Collapse
|
11
|
Lewandowska A, Ołdziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions. Proteins 2010; 78:723-37. [PMID: 19847914 DOI: 10.1002/prot.22605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A 20-residue peptide, IG(42-61), derived from the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptoccocus was studied using circular dichroism, nuclear magnetic resonance (NMR) spectroscopy at various temperatures and by differential scanning calorimetry (DSC). Unlike other related peptides studied so far, this peptide displays two heat capacity peaks in DSC measurements (at a scanning rate of 1.5 deg/min at a peptide concentration of 0.07 mM), which suggests a three-state folding/unfolding process. The results from DSC and NMR measurements suggest the formation of a dynamic network of hydrophobic interactions stabilizing the structure, which resembles a beta-hairpin shape over a wide range of temperatures (283-313 K). Our results show that IG (42-61) possesses a well-organized three-dimensional structure stabilized by long-range hydrophobic interactions (Tyr50 ... Phe57 and Trp48 ... Val59) at T = 283 K and (Trp48 ... Val59) at 305 and 313 K. The mechanism of beta-hairpin folding and unfolding, as well as the influence of peptide length on its conformational properties, are also discussed.
Collapse
Affiliation(s)
- Agnieszka Lewandowska
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | | | | | | |
Collapse
|
12
|
Lewandowska A, Ołdziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein. Biopolymers 2010; 93:469-80. [PMID: 20049918 DOI: 10.1002/bip.21365] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A 34-residue alpha/beta peptide [IG(28-61)], derived from the C-terminal part of the B3 domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the beta-hairpin in the native structure, forms structure similar to the beta-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47-Val59). On the other hand, the N-terminal part of IG(28-61), which corresponds to the middle alpha-helix in the native structure, is unstructured at low temperature (283 K) and forms an alpha-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (beta-hairpin) and the N-terminal (alpha-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726-736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed.
Collapse
Affiliation(s)
- Agnieszka Lewandowska
- University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | | | | | | |
Collapse
|
13
|
Skwierawska A, Makowska J, Ołdziej S, Liwo A, Scheraga HA. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure. Proteins 2009; 75:931-53. [PMID: 19089955 DOI: 10.1002/prot.22304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We previously studied a 16-amino acid-residue fragment of the C-terminal beta-hairpin of the B3 domain (residues 46-61), [IG(46-61)] of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG (46-61) by systematically shortening the peptide by one residue at a time from both the C- and the N-terminus. To determine the structure and stability of two resulting 12- and 14-amino acid-residue peptides, IG(48-59) and IG(47-60), respectively, we carried out circular dichroism, NMR, and calorimetric studies of these peptides in pure water. Our results show that IG(48-59) possesses organized three-dimensional structure stabilized by hydrophobic interactions (Tyr50-Phe57 and Trp48-Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (T(m) = 310 K) measured by differential scanning calorimetry (DSC). The melting temperature of IG(47-60) determined by DSC is T(m) = 330 K and its structure is similar to that of the native beta-hairpin at all (lower) temperatures examined (283-313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a beta-hairpin structural element.
Collapse
Affiliation(s)
- Agnieszka Skwierawska
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | | | | | | | | |
Collapse
|
14
|
Skwierawska A, Ołdziej S, Liwo A, Scheraga HA. Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers 2009; 91:37-51. [PMID: 18767128 DOI: 10.1002/bip.21080] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structure and stability of the 16-amino-acid-residue fragment [IG(46-61)] corresponding to the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus was investigated by means of CD and NMR spectroscopy and by differential scanning calorimetry. The CD and 2D NMR experiments were carried out (i) in water at different temperatures and (ii) at one temperature (305 K), with only CD, at different TFE concentrations. Our results show that the IG(46-61) peptide possesses organized three-dimensional structure at all investigated temperatures. The three-dimensional structure of the IG(46-61) peptide resembles the general shape of a beta-hairpin that is also observed for this peptide in the experimental structure of the B3 domain in the whole G protein; the structure is stabilized by hydrophobic interactions between nonpolar side chains. Our study shows that the melting temperature of the IG(46-61) peptide is about 320 K which supports the hypothesis that the investigated peptide can serve as a folding initiation site of the B3 domain of the immunoglobulin binding protein G.
Collapse
Affiliation(s)
- Agnieszka Skwierawska
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland
| | | | | | | |
Collapse
|
15
|
Watanabe H, Matsumaru H, Ooishi A, Feng Y, Odahara T, Suto K, Honda S. Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions. J Biol Chem 2009; 284:12373-83. [PMID: 19269963 PMCID: PMC2673305 DOI: 10.1074/jbc.m809236200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/23/2009] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interaction in response to environmental conditions enables sophisticated biological and biotechnological processes. Aiming toward the rational design of a pH-sensitive protein-protein interaction, we engineered pH-sensitive mutants of streptococcal protein G B1, a binder to the IgG constant region. We systematically introduced histidine residues into the binding interface to cause electrostatic repulsion on the basis of a rigid body model. Exquisite pH sensitivity of this interaction was confirmed by surface plasmon resonance and affinity chromatography employing a clinically used human IgG. The pH-sensitive mechanism of the interaction was analyzed and evaluated from kinetic, thermodynamic, and structural viewpoints. Histidine-mediated electrostatic repulsion resulted in significant loss of exothermic heat of the binding that decreased the affinity only at acidic conditions, thereby improving the pH sensitivity. The reduced binding energy was partly recovered by "enthalpy-entropy compensation." Crystal structures of the designed mutants confirmed the validity of the rigid body model on which the effective electrostatic repulsion was based. Moreover, our data suggested that the entropy gain involved exclusion of water molecules solvated in a space formed by the introduced histidine and adjacent tryptophan residue. Our findings concerning the mechanism of histidine-introduced interactions will provide a guideline for the rational design of pH-sensitive protein-protein recognition.
Collapse
Affiliation(s)
- Hideki Watanabe
- National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba 305-8566, Japan
| | | | | | | | | | | | | |
Collapse
|
16
|
Protein GB1 folding and assembly from structural elements. Int J Mol Sci 2009; 10:1552-1566. [PMID: 19468325 PMCID: PMC2680633 DOI: 10.3390/ijms10041552] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/20/2009] [Accepted: 03/31/2009] [Indexed: 11/17/2022] Open
Abstract
Folding of the Protein G B1 domain (PGB1) shifts with increasing salt concentration from a cooperative assembly of inherently unstructured subdomains to an assembly of partly pre-folded structures. The salt-dependence of pre-folding contributes to the stability minimum observed at physiological salt conditions. Our conclusions are based on a study in which the reconstitution of PGB1 from two fragments was studied as a function of salt concentrations and temperature using circular dichroism spectroscopy. Salt was found to induce an increase in β-hairpin structure for the C-terminal fragment (residues 41 – 56), whereas no major salt effect on structure was observed for the isolated N-terminal fragment (residues 1 – 41). In line with the increasing evidence on the interrelation between fragment complementation and stability of the corresponding intact protein, we also find that salt effects on reconstitution can be predicted from salt dependence of the stability of the intact protein. Our data show that our variant (which has the mutations T2Q, N8D, N37D and reconstitutes in a manner similar to the wild type) displays the lowest equilibrium association constant around physiological salt concentration, with higher affinity observed both at lower and higher salt concentration. This corroborates the salt effects on the stability towards denaturation of the intact protein, for which the stability at physiological salt is lower compared to both lower and higher salt concentrations. Hence we conclude that reconstitution reports on molecular factors that govern the native states of proteins.
Collapse
|
17
|
Li H, Wang HC, Cao Y, Sharma D, Wang M. Configurational Entropy Modulates the Mechanical Stability of Protein GB1. J Mol Biol 2008; 379:871-80. [DOI: 10.1016/j.jmb.2008.04.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 04/03/2008] [Accepted: 04/08/2008] [Indexed: 11/28/2022]
|
18
|
Xue WF, Carey J, Linse S. Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin. Proteins 2005; 57:586-95. [PMID: 15382228 DOI: 10.1002/prot.20241] [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: 11/10/2022]
Abstract
Accurate and precise determinations of thermodynamic parameters of binding are important steps toward understanding many biological mechanisms. Here, a multi-method approach to binding analysis is applied and a detailed error analysis is introduced. Using this approach, the binding thermodynamics and kinetics of the reconstitution of the protein monellin have been quantitatively determined in detail by simultaneous analysis of data collected with fluorescence spectroscopy, surface plasmon resonance and isothermal titration calorimetry at 25 degrees C, pH 7.0 and 150 mM NaCl. Monellin is an intensely sweet protein composed of two peptide chains that form a single globular domain. The kinetics of the reconstitution reaction are slow, with an association rate constant, k(on) of 8.8 x 10(3) M(-1) s(-1) and a dissociation rate constant, k(off) of 3.1 x 10(-4) s(-1). The equilibrium constant K(A) is 2.8 x 10(7) M(-1) corresponding to a standard free energy of association, DeltaG degrees , of -42.5 kJ/mol. The enthalpic component, DeltaH degrees , is -18.7 kJ/mol and the entropic contribution, DeltaS degrees , is 79.8 J mol(-1) K(-1) (-TDeltaS degrees = -23.8 kJ/mol). The association of monellin is therefore a bimolecular intra-protein association whose energetics are slightly dominated by entropic factors.
Collapse
Affiliation(s)
- Wei-Feng Xue
- Department of Biophysical Chemistry, Lund University, Lund, Sweden
| | | | | |
Collapse
|
19
|
Dutta S, Batori V, Koide A, Koide S. High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Sci 2005; 14:2838-48. [PMID: 16199661 PMCID: PMC2253215 DOI: 10.1110/ps.051603005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The tenth fibronectin type III (FN3) domain of human fibronectin (FNfn10), a prototype of the ubiquitous FN3 domain, is a small, monomeric beta-sandwich protein. In this study, we have bisected FNfn10 in each loop to generate a total of six fragment pairs. We found that fragment pairs bisected at multiple loops of FNfn10 show complementation in vivo as tested with a yeast two-hybrid system. The dissociation constant of these fragment pairs determined in vitro were as low as 3 nM, resulting in one of the tightest fragment complementation systems reported so far. Furthermore, we show that the affinity of fragment complementation is correlated with the stability of the uncut parent protein. Exploring this correlation, we screened a yeast two-hybrid library of one fragment and identified mutations that suppress the effect of a destabilizing mutation in the other fragment. One of the identified mutations significantly increased the stability of the uncut wild-type protein, proving that fragment complementation can be used as a novel strategy for the selection of proteins with enhanced stability.
Collapse
Affiliation(s)
- Sanjib Dutta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
20
|
Dell'Orco D, Seeber M, De Benedetti PG, Fanelli F. Probing Fragment Complementation by Rigid-Body Docking: in Silico Reconstitution of Calbindin D9k. J Chem Inf Model 2005; 45:1429-38. [PMID: 16180920 DOI: 10.1021/ci0501995] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbindin D9k, from its two EF-hands subdomains, namely, EF1 (residues 1-43) and EF2 (residues 44-75). The EF1 fragment has been used both in its wild type and in nine mutant forms, in line with in vitro experiments. Consistent with in vitro data, ZDOCK reconstituted the proper fold of wild-type and mutated calbindin, locating the nativelike structures (i.e., holding a root-mean-square deviation < 1 A with respect to the X-ray structure) among the first 10 top-scored solutions out of 4000. Moreover, the three independent in silico reconstitutions of wild-type calbindin ranked a nativelike structure at the top of the output list, that is, the best scored one. The algorithm has been also successfully challenged in reconstituting the EF2 homodimer from two identical copies of the monomer. Furthermore, quantitative models consisting of linear correlations between thermodynamic data and ZDOCK scores were built, providing a tested tool for very fast in silico predictions of the free energy of association of protein-protein complexes solved at the atomic level and known to not undergo significant conformational changes upon binding.
Collapse
Affiliation(s)
- Daniele Dell'Orco
- Department of Chemistry and Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41100 Modena, Italy
| | | | | | | |
Collapse
|
21
|
Livesay DR, Dallakyan S, Wood GG, Jacobs DJ. A flexible approach for understanding protein stability. FEBS Lett 2004; 576:468-76. [PMID: 15498582 DOI: 10.1016/j.febslet.2004.09.057] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 09/20/2004] [Indexed: 11/25/2022]
Abstract
A distance constraint model (DCM) is presented that identifies flexible regions within protein structure consistent with specified thermodynamic condition. The DCM is based on a rigorous free energy decomposition scheme representing structure as fluctuating constraint topologies. Entropy non-additivity is problematic for naive decompositions, limiting the success of heat capacity predictions. The DCM resolves non-additivity by summing over independent entropic components determined by an efficient network-rigidity algorithm. A minimal 3-parameter DCM is demonstrated to accurately reproduce experimental heat capacity curves. Free energy landscapes and quantitative stability-flexibility relationships are obtained in terms of global flexibility. Several connections to experiment are made.
Collapse
Affiliation(s)
- D R Livesay
- Department of Chemistry, California State Polytechnic University, Pomona, 3801 W Temple Ave, Pomona, CA 91768, USA
| | | | | | | |
Collapse
|
22
|
Honda S, Yamasaki K, Sawada Y, Morii H. 10 Residue Folded Peptide Designed by Segment Statistics. Structure 2004; 12:1507-18. [PMID: 15296744 DOI: 10.1016/j.str.2004.05.022] [Citation(s) in RCA: 237] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Revised: 05/18/2004] [Accepted: 05/25/2004] [Indexed: 11/25/2022]
Abstract
We have designed a peptide termed chignolin, consisting of only 10 amino acid residues (GYDPETGTWG), on the basis of statistics derived from more than 10,000 protein segments. The peptide folds into a unique structure in water and shows a cooperative thermal transition, both of which may be hallmarks of a protein. Also, the experimentally determined beta-hairpin structure was very close to what we had targeted. The performance of the short peptide not only implies that the methodology employed here can contribute toward development of novel techniques for protein design, but it also yields insights into the raison d'etre of an autonomous element involved in a natural protein. This is of interest for the pursuit of folding mechanisms and evolutionary processes of proteins.
Collapse
Affiliation(s)
- Shinya Honda
- National Institute of Advanced Industrial Science and Technology, AIST Central 6, Tsukuba 305-8566, Japan.
| | | | | | | |
Collapse
|
23
|
He J, Zhang Z, Shi Y, Liu H. Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions. J Chem Phys 2003. [DOI: 10.1063/1.1591717] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
24
|
Santiveri CM, Santoro J, Rico M, Jiménez MA. Thermodynamic analysis of beta-hairpin-forming peptides from the thermal dependence of (1)H NMR chemical shifts. J Am Chem Soc 2002; 124:14903-9. [PMID: 12475331 DOI: 10.1021/ja0278537] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The temperature dependence of the (1)H chemical shifts of six designed peptides previously shown to adopt beta-hairpin structures in aqueous solution has been analyzed in terms of two-state (beta-hairpin left arrow over right arrow coil) equilibrium. The stability of the beta-hairpins formed by these peptides, as derived from their T(m) (midpoint transition temperature) values, parallels in general their ability to adopt those structures as deduced from independent NMR parameters: NOEs, Deltadelta(C)(alpha)(H), Deltadelta(C)(alpha), and Deltadelta(C)(beta) values. The observed T(m) values are dependent on the particular position within the beta-hairpin that is probed, indicating that their folding to a beta-hairpin conformation deviates from a "true" two-state transition. To obtain individual T(m) values for each hairpin region in each peptide, a simplified model of a successive uncoupled two-state equilibrium covering the entire process has been applied. The distribution of T(m) values obtained for the different beta-hairpin regions (turn, strands, backbone, side chains) in the six analyzed peptides reveals a similar pattern. A model for beta-hairpin folding is proposed on the basis of this pattern and the reasonable assumption that regions showing higher T(m) values are the last ones to unfold and, presumably, the first to form. With this assumption, the analysis suggests that turn formation is the first event in beta-hairpin folding. This is consistent with previous results on the essential role of the turn sequence in beta-hairpin folding.
Collapse
Affiliation(s)
- Clara M Santiveri
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid, Spain
| | | | | | | |
Collapse
|
25
|
|
26
|
Ojennus DD, Fleissner MR, Wuttke DS. Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear NMR. Protein Sci 2001; 10:2162-75. [PMID: 11604523 PMCID: PMC2374061 DOI: 10.1110/ps.18701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2001] [Revised: 07/16/2001] [Accepted: 07/25/2001] [Indexed: 10/14/2022]
Abstract
The N-terminal SH2 domain from the p85alpha subunit of phosphatidylinositol 3' kinase is cleaved specifically into 9- and 5-kD fragments by limited proteolytic digestion with trypsin. The noncovalent SH2 domain complex and its constituent tryptic peptides have been investigated using high-resolution heteronuclear magnetic resonance (NMR). These studies have established the viability of the SH2 domain as a fragment complementation system. The individual peptide fragments are predominantly unstructured in solution. In contrast, the noncovalent 9-kD + 5-kD complex shows a native-like (1)H-(15)N HSQC spectrum, demonstrating that the two fragments fold into a native-like structure on binding. Chemical shift analysis of the noncovalent complex compared to the native SH2 domain reveals that the highest degree of perturbation in the structure occurs at the cleavage site within a flexible loop and along the hydrophobic interface between the two peptide fragments. Mapping of these chemical shift changes on the structure of the domain reveals changes consistent with the reduction in affinity for the target peptide ligand observed in the noncovalent complex relative to the intact protein. The 5-kD fragment of the homologous Src protein is incapable of structurally complementing the p85 9-kD fragment, either in complex formation or in the context of the full-length protein. These high-resolution structural studies of the SH2 domain fragment complementation features establish the suitability of the system for further protein-folding and design studies.
Collapse
Affiliation(s)
- D D Ojennus
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
| | | | | |
Collapse
|
27
|
Burgess K, Han I, Zhang A, Zheng WH, Shanmugam K, Featherstone MS, Saragovi HU. DiSSiMiL: Diverse Small Size Mini-Libraries applied to simple and rapid epitope mapping of a monoclonal antibody. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2001; 57:68-76. [PMID: 11168890 DOI: 10.1034/j.1399-3011.2001.00786.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methods for screening protein-protein interactions are useful in protein science and for the generation of drug leads. We set out to develop a simplified assay to rapidly test protein-protein interactions, with a library of 400 pentapeptides comprising the 20 natural amino acids at two variable positions followed by three glycines (NH2-X1X2GGG). The library was used to identify the epitope of monoclonal antibody (mAb) 10D11 directed against the HOXD4 protein. Three pentapeptide 'hits' were selected (VYGGG, PWGGG and WKGGG) from direct binding assays screening for pentapeptide-mAb interactions; and from assays using pentapeptides in solution to competitively block HOXD4-mAb interactions. Alignment of the three 'hit' pentapeptides to the HOXD4 sequence predicts the mAb 10D11 epitope as NH2-VYPWMK. Synthesis of NH2-VYPWMK hexapeptide confirmed this prediction; and an alanine scan of HOXD4 ablated binding by mAb 10D11 when amino acids in the putative epitope were mutated. We propose that these simplified but diverse libraries can be used for rapid epitope mapping of some mAbs, and for generating lead small peptide analogs that interfere with receptor-ligand or other protein-protein interactions, or with enzymatic activity.
Collapse
Affiliation(s)
- K Burgess
- Department Chemistry, Texas A&M University, College Station, USA
| | | | | | | | | | | | | |
Collapse
|
28
|
Narita M, Mochizuki A, Ohuchi S. Assingments of Tri- and Tetrapeptide Sequences in Globular Proteins to the 18 Kinds of Local Structures along Helices and Their Propensities for Specific Local Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2000. [DOI: 10.1246/bcsj.73.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
29
|
Honda S, Kobayashi N, Munekata E. Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol 2000; 295:269-78. [PMID: 10623525 DOI: 10.1006/jmbi.1999.3346] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To elucidate early nucleation stages in protein folding, multi-probed thermodynamic characterization was applied to the beta-hairpin structural formation of G-peptide, which is a C-terminal fragment of the B1 domain of streptococcal protein G. The segment corresponding to the sequence of G-peptide is believed to act as a nucleus during the folding process of the B1 domain. In spite of the broad thermal transition of G-peptide, nuclear magnetic resonance (NMR) melting measurements combined with our original analytical theory enabled us to obtain the thermodynamic properties of the beta-hairpin formation with considerable accuracy. Additionally, all the thermodynamic properties determined by every NMR probe on both the main-chain and the side-chains were quite similar, and also comparable to the values that were independently determined by calorimetric analysis of G-peptide. These results demonstrate that G-peptide folds cooperatively throughout the molecule. In other words, the formation of the beta-hairpin is interpreted as the fashion of a first-order phase transition between two states without any distinguishable intermediates. This cooperative formation of the short linear peptide consisting of only 16 residues provides insight into not only the first folding events of the B1 domain, but also the general principles of proteins in terms of structural hierarchy, stability and folding mechanism.
Collapse
Affiliation(s)
- S Honda
- National Institute of Bioscience and Human Technology, Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | | | | |
Collapse
|
30
|
Honda S, Uedaira H, Vonderviszt F, Kidokoro S, Namba K. Folding energetics of a multidomain protein, flagellin. J Mol Biol 1999; 293:719-32. [PMID: 10543962 DOI: 10.1006/jmbi.1999.3175] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thermodynamic investigations of flagellin from Salmonella typhimurium and its proteolytic fragments were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements. A new method of analysis for a multi-state transition based on our original theoretical treatment of thermodynamic equations has been developed to analyze those data. The analysis of DSC curves confirmed the three thermodynamic domains of flagellin. The thermodynamic parameters of each domain were revised from those previously reported and the new values of the parameters have a good correlation to the apparent molecular masses of the morphological domains. CD melting measurements at far and near-UV wavelengths showed sequential unfolding of the domains. Therefore, we could reasonably assign the thermodynamically identified domains to the morphological domains. Further analysis of both DSC and CD data provided insights into the folding energetics of the multidomain structure of flagellin. An inner domain (Df1) of flagellin in the filament unfolds through a relatively broad transition, while the two outer domains unfold cooperatively and show sharp transitions. This indicates that the interdomain interactions between Df1 and D2 has different characteristics from the apparently more intimate interactions between D2 and D3. These characteristics suggest that flagellin is organized with relatively flexible domains and rigid domains, which appears to be responsible for the well-regulated assembly mechanism of the bacterial flagellar filament.
Collapse
Affiliation(s)
- S Honda
- National Institute of Bioscience and Human-Technology, Higashi, Tsukuba, 305-8566, Japan.
| | | | | | | | | |
Collapse
|
31
|
Beligere GS, Dawson PE. Conformationally Assisted Protein Ligation Using C-Terminal Thioester Peptides. J Am Chem Soc 1999. [DOI: 10.1021/ja9907919] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gangamani S. Beligere
- Departments of Cell Biology and Chemistry The Skaggs Institute for Chemical Biology The Scripps Research Institute La Jolla, California 92037
| | - Philip E. Dawson
- Departments of Cell Biology and Chemistry The Skaggs Institute for Chemical Biology The Scripps Research Institute La Jolla, California 92037
| |
Collapse
|