1
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Richaud AD, Mandal S, Das A, Roche SP. Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides. ACS Chem Biol 2023; 18:2555-2563. [PMID: 37976523 DOI: 10.1021/acschembio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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2
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Chen G, Wang H, Bumba L, Masin J, Sebo P, Li H. The adenylate cyclase toxin RTX domain follows a series templated folding mechanism with implications for toxin activity. J Biol Chem 2023; 299:105150. [PMID: 37567473 PMCID: PMC10511787 DOI: 10.1016/j.jbc.2023.105150] [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: 03/17/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Folding of the Repeats-in-toxin (RTX) domain of the bacterial adenylate cyclase toxin-hemolysin (CyaA) is critical to its toxin activities and the virulence of the whooping cough agent Bordetella pertussis. The RTX domain (RD) contains five RTX blocks (RTX-i to RTX-v) and their folding is driven by the binding of calcium. However, the detailed molecular mechanism via which the folding signal transmits within the five RTX blocks remains unknown. By combining single molecule optical tweezers, protein engineering, and toxin activity assays, here we demonstrate that the folding of the RD follows a strict hierarchy, with the folding starting from its C-terminal block RTX-v and proceeding towards the N-terminal RTX-i block sequentially. Our results reveal a strict series, templated folding mechanism, where the folding signal is transmitted along the RD in a series fashion from its C terminus continuously to the N terminus. Due to the series nature of this folding signal transmission pathway, the folding of RD can be disrupted at any given RTX block, rendering the RTX blocks located N-terminally to the disruption site and the acylation region of CyaA unfolded and abolishing CyaA's toxin activities. Our results reveal key mechanistic insights into the secretion and folding process of CyaA and may open up new potential avenues towards designing new therapeutics to abolish toxin activity of CyaA and combat B. pertussis.
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Affiliation(s)
- Guojun Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Han Wang
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Jiri Masin
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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3
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Skokowa J, Hernandez Alvarez B, Coles M, Ritter M, Nasri M, Haaf J, Aghaallaei N, Xu Y, Mir P, Krahl AC, Rogers KW, Maksymenko K, Bajoghli B, Welte K, Lupas AN, Müller P, ElGamacy M. A topological refactoring design strategy yields highly stable granulopoietic proteins. Nat Commun 2022; 13:2948. [PMID: 35618709 PMCID: PMC9135769 DOI: 10.1038/s41467-022-30157-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 04/19/2022] [Indexed: 11/09/2022] Open
Abstract
Protein therapeutics frequently face major challenges, including complicated production, instability, poor solubility, and aggregation. De novo protein design can readily address these challenges. Here, we demonstrate the utility of a topological refactoring strategy to design novel granulopoietic proteins starting from the granulocyte-colony stimulating factor (G-CSF) structure. We change a protein fold by rearranging the sequence and optimising it towards the new fold. Testing four designs, we obtain two that possess nanomolar activity, the most active of which is highly thermostable and protease-resistant, and matches its designed structure to atomic accuracy. While the designs possess starkly different sequence and structure from the native G-CSF, they show specific activity in differentiating primary human haematopoietic stem cells into mature neutrophils. The designs also show significant and specific activity in vivo. Our topological refactoring approach is largely independent of sequence or structural context, and is therefore applicable to a wide range of protein targets. Skokowa et al. reconstruct the fold of a granulopoietic cytokine, resulting in de novo, hyperstable, highly active proteins with therapeutic potential for treating several neutropenia disorders.
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Affiliation(s)
- Julia Skokowa
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany.
| | | | - Murray Coles
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Malte Ritter
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Masoud Nasri
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Jérémy Haaf
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Narges Aghaallaei
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Yun Xu
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Perihan Mir
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Ann-Christin Krahl
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Katherine W Rogers
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kateryna Maksymenko
- Max Planck Institute for Biology, 72076, Tübingen, Germany.,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany
| | - Baubak Bajoghli
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Karl Welte
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany.,Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Mohammad ElGamacy
- Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076, Tübingen, Germany. .,Friedrich Miescher Laboratory of the Max Planck Society, 72076, Tübingen, Germany. .,Heliopolis Biotechnology Ltd, Cambridge, CB24 9RX, UK. .,Max Planck Institute for Biology, 72076, Tübingen, Germany.
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4
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Wang H, Chen G, Li H. Templated folding of the RTX domain of the bacterial toxin adenylate cyclase revealed by single molecule force spectroscopy. Nat Commun 2022; 13:2784. [PMID: 35589788 PMCID: PMC9120197 DOI: 10.1038/s41467-022-30448-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
The RTX (repeats-in-toxin) domain of the bacterial toxin adenylate cyclase (CyaA) contains five RTX blocks (RTX-i to RTX-v) and its folding is essential for CyaA’s functions. It was shown that the C-terminal capping structure of RTX-v is critical for the whole RTX to fold. However, it is unknown how the folding signal transmits within the RTX domain. Here we use optical tweezers to investigate the interplay between the folding of RTX-iv and RTX-v. Our results show that RTX-iv alone is disordered, but folds into a Ca2+-loaded-β-roll structure in the presence of a folded RTX-v. Folding trajectories of RTX-iv-v reveal that the folding of RTX-iv is strictly conditional upon the folding of RTX-v, suggesting that the folding of RTX-iv is templated by RTX-v. This templating effect allows RTX-iv to fold rapidly, and provides significant mutual stabilization. Our study reveals a possible mechanism for transmitting the folding signal within the RTX domain. The authors use optical tweezers to show that the folding of repeats-in-toxin (RTX) block-iv in adenylate cyclase is templated by the folded RTX block-v. The findings suggest a possible mechanism for transmitting the folding signal in the RTX domain.
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Affiliation(s)
- Han Wang
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.,State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, 300072, Tianjin, P. R. China
| | - Guojun Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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5
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Baxa MC, Sosnick TR. Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis. Methods Mol Biol 2022; 2376:31-63. [PMID: 34845602 DOI: 10.1007/978-1-0716-1716-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of the transition state ensemble (TSE) represents the rate-limiting step in protein folding. The TSE is the least populated state on the pathway, and its characterization remains a challenge. Properties of the TSE can be inferred from the effects on folding and unfolding rates for various perturbations. A difficulty remains on how to translate these kinetic effects to structural properties of the TSE. Several factors can obscure the translation of point mutations in the frequently used method, "mutational Phi analysis." We take a complementary approach in "Psi analysis," employing rationally inserted metal binding sites designed to probe pairwise contacts in the TSE. These contacts can be confidently identified and used to construct structural models of the TSE. The method has been applied to multiple proteins and consistently produces a considerably more structured and native-like TSE than Phi analysis. This difference has significant implications to our understanding of protein folding mechanisms. Here we describe the application of the method and discuss how it can be used to study other conformational transitions such as binding.
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Affiliation(s)
- Michael C Baxa
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
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6
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Zhang J, Wong SHD, Wu X, Lei H, Qin M, Shi P, Wang W, Bian L, Cao Y. Engineering Photoresponsive Ligand Tethers for Mechanical Regulation of Stem Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2105765. [PMID: 34561928 DOI: 10.1002/adma.202105765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Regulating stem cell functions by precisely controlling the nanoscale presentation of bioactive ligands has a substantial impact on tissue engineering and regenerative medicine but remains a major challenge. Here it is shown that bioactive ligands can become mechanically "invisible" by increasing their tether lengths to the substrate beyond a critical length, providing a way to regulate mechanotransduction without changing the biochemical conditions. Building on this finding, light switchable tethers are rationally designed, whose lengths can be modulated reversibly by switching a light-responsive protein, pdDronpa, in between monomer and dimer states. This allows the regulation of the adhesion, spreading, and differentiation of stem cells by light on substrates of well-defined biochemical and physical properties. Spatiotemporal regulation of differential cell fates on the same substrate is further demonstrated, which may represent an important step toward constructing complex organoids or mini tissues by spatially defining the mechanical cues of the cellular microenvironment with light.
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Affiliation(s)
- Junsheng Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Xin Wu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210093, China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Peng Shi
- School of Biomedical Sciences and EngineeringSouth China University of Technology, Guangzhou International Campus, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
| | - Liming Bian
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
- School of Biomedical Sciences and EngineeringSouth China University of Technology, Guangzhou International Campus, Guangzhou, 511442, P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, P. R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210093, China
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7
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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8
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Do PC, Nguyen TH, Vo UHM, Le L. iBRAB: In silico based-designed broad-spectrum Fab against H1N1 influenza A virus. PLoS One 2020; 15:e0239112. [PMID: 33382708 PMCID: PMC7774956 DOI: 10.1371/journal.pone.0239112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
Influenza virus A is a significant agent involved in the outbreak of worldwide epidemics, causing millions of fatalities around the world by respiratory diseases and seasonal illness. Many projects had been conducting to investigate recovered infected patients for therapeutic vaccines that have broad-spectrum activity. With the aid of the computational approach in biology, the designation for a vaccine model is more accessible. We developed an in silico protocol called iBRAB to design a broad-reactive Fab on a wide range of influenza A virus. The Fab model was constructed based on sequences and structures of available broad-spectrum Abs or Fabs against a wide range of H1N1 influenza A virus. As a result, the proposed Fab model followed iBRAB has good binding affinity over 27 selected HA of different strains of H1 influenza A virus, including wild-type and mutated ones. The examination also took by computational tools to fasten the procedure. This protocol could be applied for a fast-designed therapeutic vaccine against different types of threats.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Binding Sites
- Computer Simulation
- Drug Design
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/biosynthesis
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Molecular Docking Simulation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Sequence Alignment
- Sequence Homology, Amino Acid
- Thermodynamics
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Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Trung H. Nguyen
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Uyen H. M. Vo
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Thu Duc District, Hochiminh City, Vietnam
- Vietnam National University Ho Chi Minh City, Thu Duc District, Hochiminh City, Vietnam
- Vingroup Big Data Institute, Hai Ba Trung District, Ha Noi, Vietnam
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9
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Uehara R, Dan N, Amesaka H, Yoshizawa T, Koga Y, Kanaya S, Takano K, Matsumura H, Tanaka SI. Insertion loop-mediated folding propagation governs efficient maturation of hyperthermophilic Tk-subtilisin at high temperatures. FEBS Lett 2020; 595:452-461. [PMID: 33314039 DOI: 10.1002/1873-3468.14028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 11/05/2022]
Abstract
The serine protease Tk-subtilisin from the hyperthermophilic archaeon Thermococcus kodakarensis possesses three insertion loops (IS1-IS3) on its surface, as compared to its mesophilic counterparts. Although IS1 and IS2 are required for maturation of Tk-subtilisin at high temperatures, the role of IS3 remains unknown. Here, CD spectroscopy revealed that IS3 deletion arrested Tk-subtilisin folding at an intermediate state, in which the central nucleus was formed, but the subsequent folding propagation into terminal subdomains did not occur. Alanine substitution of the aspartate residue in IS3 disturbed the intraloop hydrogen-bonding network, as evidenced by crystallographic analysis, resulting in compromised folding at high temperatures. Taking into account the high conservation of IS3 across hyperthermophilic homologues, we propose that the presence of IS3 is important for folding of hyperthermophilic subtilisins in high-temperature environments.
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Affiliation(s)
- Ryo Uehara
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan.,Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga, Japan.,Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Nanako Dan
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Hiroshi Amesaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan.,Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga, Japan
| | - Shun-Ichi Tanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Shiga, Japan.,Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga, Japan.,Department of Biomolecular Chemistry, Kyoto Prefectural University, Japan
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10
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Ripka JF, Perez-Riba A, Chaturbedy PK, Itzhaki LS. Testing the length limit of loop grafting in a helical repeat protein. Curr Res Struct Biol 2020; 3:30-40. [PMID: 34235484 PMCID: PMC8244534 DOI: 10.1016/j.crstbi.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Alpha-helical repeat proteins such as consensus-designed tetratricopeptide repeats (CTPRs) are exceptionally stable molecules that are able to tolerate destabilizing sequence alterations and are therefore becoming increasingly valued as a modular platform for biotechnology and biotherapeutic applications. A simple approach to functionalize the CTPR scaffold that we are pioneering is the insertion of short linear motifs (SLiMs) into the loops between adjacent repeats. Here, we test the limits of the scaffold by inserting 17 highly diverse amino acid sequences of up to 58 amino acids in length into a two-repeat protein and examine the impact on protein folding, stability and solubility. The sequences include three SLiMs that bind oncoproteins and eleven naturally occurring linker sequences all predicted to be intrinsically disordered but with conformational preferences ranging from compact globules to expanded coils. We show that the loop-grafted proteins retain the native CTPR structure and are thermally stable with melting temperatures above 60 °C, despite the longest loop sequence being almost the same size as the CTPR scaffold itself (68 amino acids). Although the main determinant of the effect of stability was found to be loop length and was relatively insensitive to amino acid composition, the relationship between protein solubility and the loop sequences was more complex, with the presence of negatively charged amino acids enhancing the solubility. Our findings will help us to fully realize the potential of the repeat-protein scaffold, allowing a rational design approach to create artificial modular proteins with customized functional capabilities.
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Key Words
- CD, circular dichroism
- CTPRs, consensus-designed tetratricopeptide repeats
- FCR, fraction of charged residues
- IDPs, intrinsically disordered proteins
- IDRs, intrinsically disordered regions
- Intrinsically disordered protein
- Intrinsically disordered region
- NCPR, net charge per residue
- PBIP1, polo-box interacting protein 1
- Peptide grafting
- SLiMs, short linear motifs
- TBP, tankyrase-binding peptides
- Tandem-repeat protein
- Tetratricopeptide repeat
- ves, effective solvation volume
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Affiliation(s)
- Juliane F. Ripka
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Piyush K. Chaturbedy
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Laura S. Itzhaki
- Department of Pharmacology University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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11
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Linse S, Thulin E, Nilsson H, Stigler J. Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding. Sci Rep 2020; 10:20108. [PMID: 33208843 PMCID: PMC7674454 DOI: 10.1038/s41598-020-76598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/26/2020] [Indexed: 11/12/2022] Open
Abstract
Protein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.
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Affiliation(s)
- Sara Linse
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden.
| | - Eva Thulin
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Hanna Nilsson
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Johannes Stigler
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden. .,Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany.
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12
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Affiliation(s)
- Lavi S. Bigman
- Department of Structural BiologyWeizmann Institute of Science Rehovot 76100 Israel
| | - Yaakov Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 76100 Israel
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13
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Pavlenko OS, Gra OA, Mustafaev ON, Kabarbaeva KV, Sadovskaya NS, Tyurin AA, Fadeev VS, Goldenkova-Pavlova IV. Thermostable Lichenase from Clostridium thermocellum as a Host Protein in the Domain Insertion Approach. BIOCHEMISTRY. BIOKHIMIIA 2019; 84:931-940. [PMID: 31522675 DOI: 10.1134/s0006297919080091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
Abstract
Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.73 (P29716)) has been tested for the insertion of two model fluorescent proteins (EGFP and TagRFP) into two regions of this enzyme. Functional folding of the resulting proteins was confirmed by retention of lichenase activity and EGFP and TagRFP fluorescence. These results convincingly demonstrate that (i) the two experimentally selected lichenase loop regions may serve as the areas for domain insertion without disturbing enzyme folding in vivo; (ii) lichenase permits not only single but also tandem insertions of large protein domains. High specific activity, outstanding thermostability, and efficient in vitro refolding of thermostable lichenase make it an attractive new host protein for the insertional fusion of domains in the engineering of multifunctional proteins.
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Affiliation(s)
- O S Pavlenko
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
| | - O A Gra
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - O N Mustafaev
- Baku State University, Department of Biophysics and Molecular Biology, Baku, AZ1106, Azerbaijan.
| | - K V Kabarbaeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - N S Sadovskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - A A Tyurin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - V S Fadeev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - I V Goldenkova-Pavlova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
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14
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Gavrilov Y, Dagan S, Reich Z, Scherf T, Levy Y. An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation. J Phys Chem B 2018; 122:10855-10860. [PMID: 30411894 DOI: 10.1021/acs.jpcb.8b09658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Previous studies conducted on flexible loop regions in proteins revealed that the energetic consequences of changing loop length predominantly arise from the entropic cost of ordering a loop during folding. However, in an earlier study of human acylphosphatase (hmAcP) using experimental and computational approaches, we showed that thermodynamic stabilization upon loop truncation can be attributed mainly to the increased entropy of the folded state. Here, using 15N NMR spectroscopy, we studied the effect of loop truncation on hmAcP backbone dynamics on the picosecond-nanosecond timescale with the aim of confirming the effect of folded state entropy on protein stability. NMR-relaxation-derived N-H squared generalized order parameters reveal that loop truncation results in a significant increase in protein conformational flexibility. Comparison of these results with previously acquired all-atom molecular dynamics simulation, analyzed here in terms of squared generalized NMR order parameters, demonstrates general agreement between the two methods. The NMR study not only provides direct evidence for the enhanced conformational entropy of the folded state of hmAcP upon loop truncation but also gives a quantitative measure of the observed effects.
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15
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Yang F, Wang H, Logan DT, Mu X, Danielsson J, Oliveberg M. The Cost of Long Catalytic Loops in Folding and Stability of the ALS-Associated Protein SOD1. J Am Chem Soc 2018; 140:16570-16579. [PMID: 30359015 DOI: 10.1021/jacs.8b08141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A conspicuous feature of the amyotrophic lateral sclerosis (ALS)-associated protein SOD1 is that its maturation into a functional enzyme relies on local folding of two disordered loops into a catalytic subdomain. To drive the disorder-to-order transition, the protein employs a single Zn2+ ion. The question is then if the entropic penalty of maintaining such disordered loops in the immature apoSOD1 monomer is large enough to explain its unusually low stability, slow folding, and pathological aggregation in ALS. To find out, we determined the effects of systematically altering the SOD1-loop lengths by protein redesign. The results show that the loops destabilize the apoSOD1 monomer by ∼3 kcal/mol, rendering the protein marginally stable and accounting for its aggregation behavior. Yet the effect on the global folding kinetics remains much smaller with a transition-state destabilization of <1 kcal/mol. Notably, this 1/3 transition-state to folded-state stability ratio provides a clear-cut example of the enigmatic disagreement between the Leffler α value from loop-length alterations (typically 1/3) and the "standard" reaction coordinates based on solvent perturbations (typically >2/3). Reconciling the issue, we demonstrate that the disagreement disappears when accounting for the progressive loop shortening that occurs along the folding pathway. The approach assumes a consistent Flory loop entropy scaling factor of c = 1.48 for both equilibrium and kinetic data and has the added benefit of verifying the tertiary interactions of the folding nucleus as determined by phi-value analysis. Thus, SOD1 not only represents a case where evolution of key catalytic function has come with the drawback of a destabilized apo state but also stands out as a well-suited model system for exploring the physicochemical details of protein self-organization.
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Affiliation(s)
- Fan Yang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Huabing Wang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Derek T Logan
- Division of Biochemistry & Structural Biology, Department of Chemistry , Lund University , Box 124, 22100 Lund , Sweden
| | - Xin Mu
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences , Stockholm University , S-106 91 Stockholm , Sweden
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16
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The structural basis of nanobody unfolding reversibility and thermoresistance. Sci Rep 2018; 8:7934. [PMID: 29784954 PMCID: PMC5962586 DOI: 10.1038/s41598-018-26338-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/10/2018] [Indexed: 12/17/2022] Open
Abstract
Nanobodies represent the variable binding domain of camelid heavy-chain antibodies and are employed in a rapidly growing range of applications in biotechnology and biomedicine. Their success is based on unique properties including their reported ability to reversibly refold after heat-induced denaturation. This view, however, is contrasted by studies which involve irreversibly aggregating nanobodies, asking for a quantitative analysis that clearly defines nanobody thermoresistance and reveals the determinants of unfolding reversibility and aggregation propensity. By characterizing nearly 70 nanobodies, we show that irreversible aggregation does occur upon heat denaturation for the large majority of binders, potentially affecting application-relevant parameters like stability and immunogenicity. However, by deriving aggregation propensities from apparent melting temperatures, we show that an optional disulfide bond suppresses nanobody aggregation. This effect is further enhanced by increasing the length of a complementarity determining loop which, although expected to destabilize, contributes to nanobody stability. The effect of such variations depends on environmental conditions, however. Nanobodies with two disulfide bonds, for example, are prone to lose their functionality in the cytosol. Our study suggests strategies to engineer nanobodies that exhibit optimal performance parameters and gives insights into general mechanisms which evolved to prevent protein aggregation.
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17
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Rodríguez-Bolaños M, Cabrera N, Perez-Montfort R. Identification of the critical residues responsible for differential reactivation of the triosephosphate isomerases of two trypanosomes. Open Biol 2017; 6:rsob.160161. [PMID: 27733588 PMCID: PMC5090059 DOI: 10.1098/rsob.160161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
The reactivation of triosephosphate isomerase (TIM) from unfolded monomers induced by guanidine hydrochloride involves different amino acids of its sequence in different stages of protein refolding. We describe a systematic mutagenesis method to find critical residues for certain physico-chemical properties of a protein. The two similar TIMs of Trypanosoma brucei and Trypanosoma cruzi have different reactivation velocities and efficiencies. We used a small number of chimeric enzymes, additive mutants and planned site-directed mutants to produce an enzyme from T. brucei with 13 mutations in its sequence, which reactivates fast and efficiently like wild-type (WT) TIM from T. cruzi, and another enzyme from T. cruzi, with 13 slightly altered mutations, which reactivated slowly and inefficiently like the WT TIM of T. brucei. Our method is a shorter alternative to random mutagenesis, saturation mutagenesis or directed evolution to find multiple amino acids critical for certain properties of proteins.
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Affiliation(s)
- Monica Rodríguez-Bolaños
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
| | - Ruy Perez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510 México DF, México
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18
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Heo S, Lee J, Joo K, Shin HC, Lee J. Protein Loop Structure Prediction Using Conformational Space Annealing. J Chem Inf Model 2017; 57:1068-1078. [DOI: 10.1021/acs.jcim.6b00742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seungryong Heo
- School
of Systems Biomedical Science, Soongsil University, Seoul 06978, Korea
| | - Juyong Lee
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | | | - Hang-Cheol Shin
- School
of Systems Biomedical Science, Soongsil University, Seoul 06978, Korea
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19
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Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017; 7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss.
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Affiliation(s)
- Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Chia-Yun Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Ru Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
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20
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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21
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Gavrilov Y, Dagan S, Levy Y. Shortening a loop can increase protein native state entropy. Proteins 2015; 83:2137-46. [PMID: 26369935 DOI: 10.1002/prot.24926] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/20/2015] [Accepted: 09/01/2015] [Indexed: 01/31/2023]
Abstract
Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shlomi Dagan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
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22
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Kwa LG, Wensley BG, Alexander CG, Browning SJ, Lichman BR, Clarke J. The folding of a family of three-helix bundle proteins: spectrin R15 has a robust folding nucleus, unlike its homologous neighbours. J Mol Biol 2014; 426:1600-10. [PMID: 24373753 PMCID: PMC3988883 DOI: 10.1016/j.jmb.2013.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 11/13/2022]
Abstract
Three homologous spectrin domains have remarkably different folding characteristics. We have previously shown that the slow-folding R16 and R17 spectrin domains can be altered to resemble the fast folding R15, in terms of speed of folding (and unfolding), landscape roughness and folding mechanism, simply by substituting five residues in the core. Here we show that, by contrast, R15 cannot be engineered to resemble R16 and R17. It is possible to engineer a slow-folding version of R15, but our analysis shows that this protein neither has a rougher energy landscape nor does change its folding mechanism. Quite remarkably, R15 appears to be a rare example of a protein with a folding nucleus that does not change in position or in size when its folding nucleus is disrupted. Thus, while two members of this protein family are remarkably plastic, the third has apparently a restricted folding landscape.
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Affiliation(s)
- Lee Gyan Kwa
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Beth G Wensley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Crispin G Alexander
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Stuart J Browning
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Benjamin R Lichman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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23
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Kumar TKS, Sivaraman T, Samuel D, Srisailam S, Ganesh G, Hsieh HC, Hung KW, Peng HJ, Ho MC, Arunkumar AI, Yu C. Protein Folding and β-Sheet Proteins. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200000141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Adhikari AN, Freed KF, Sosnick TR. Simplified protein models: predicting folding pathways and structure using amino acid sequences. PHYSICAL REVIEW LETTERS 2013; 111:028103. [PMID: 23889448 PMCID: PMC4047675 DOI: 10.1103/physrevlett.111.028103] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate the ability of simultaneously determining a protein's folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or "foldons." Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.
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Affiliation(s)
- Aashish N. Adhikari
- Department of Chemistry, University of Chicago, Chicago, IL 60637 USA
- James Franck Institute, University of Chicago, Chicago, IL 60637 USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637 USA
| | - Karl F. Freed
- Department of Chemistry, University of Chicago, Chicago, IL 60637 USA
- James Franck Institute, University of Chicago, Chicago, IL 60637 USA
- Computation Institute, University of Chicago, Chicago, IL 60637 USA
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637 USA
- Computation Institute, University of Chicago, Chicago, IL 60637 USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637 USA
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25
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Dagan S, Hagai T, Gavrilov Y, Kapon R, Levy Y, Reich Z. Stabilization of a protein conferred by an increase in folded state entropy. Proc Natl Acad Sci U S A 2013; 110:10628-33. [PMID: 23754389 PMCID: PMC3696814 DOI: 10.1073/pnas.1302284110] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Entropic stabilization of native protein structures typically relies on strategies that serve to decrease the entropy of the unfolded state. Here we report, using a combination of experimental and computational approaches, on enhanced thermodynamic stability conferred by an increase in the configurational entropy of the folded state. The enhanced stability is observed upon modifications of a loop region in the enzyme acylphosphatase and is achieved despite significant enthalpy losses. The modifications that lead to increased stability, as well as those that result in destabilization, however, strongly compromise enzymatic activity, rationalizing the preservation of the native loop structure even though it does not provide the protein with maximal stability or kinetic foldability.
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Affiliation(s)
| | - Tzachi Hagai
- Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yulian Gavrilov
- Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Yaakov Levy
- Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ziv Reich
- Departments of Biological Chemistry and
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26
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Abstract
Recent experiments have conclusively shown that proteins are able to fold from an unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones. These experiments are consistent with a growing body of theoretical work showing that a funneled, minimally frustrated energy landscape is sufficient to fold small proteins with complex topologies. Here, we present a theoretical investigation of the folding of a knotted protein, 2ouf, engineered in the laboratory by a domain fusion that mimics an evolutionary pathway for knotted proteins. Unlike a previously studied knotted protein of similar length, we see reversible folding/knotting and a surprising lack of deep topological traps with a coarse-grained structure-based model. Our main interest is to investigate how evolution might further select the geometry and stiffness of the threading region of the newly fused protein. We compare the folding of the wild-type protein to several mutants. Similarly to the wild-type protein, all mutants show robust and reversible folding, and knotting coincides with the transition state ensemble. As observed experimentally, our simulations show that the knotted protein folds about ten times slower than an unknotted construct with an identical contact map. Simulated folding kinetics reflect the experimentally observed rollover in the folding limbs of chevron plots. Successful folding of the knotted protein is restricted to a narrow range of temperature as compared to the unknotted protein and fits of the kinetic folding data below folding temperature suggest slow, nondiffusive dynamics for the knotted protein.
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27
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Shandiz AT, Baxa MC, Sosnick TR. A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable. Protein Sci 2012; 21:819-27. [PMID: 22528473 DOI: 10.1002/pro.2065] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/19/2012] [Accepted: 03/19/2012] [Indexed: 11/09/2022]
Abstract
Using a combined crosslinking-ψ analysis strategy, we examine whether the structural content of the transition state of ubiquitin can be altered. A synthetic dichloroacetone crosslink is first introduced across two β strands. Whether the structural content in the transition state ensemble has shifted towards the region containing the crosslink is probed by remeasuring the ψ value at another region (ψ identifies the degree to which an inserted bi-Histidine metal ion binding site is formed in the transition state). For sites around the periphery of the obligate transition state nucleus, we find that the resulting changes in ψ values are near or at our detection limit, thereby indicating that the structural content of the transition state has not measurably changed upon crosslinking. This work demonstrates the utility of the simultaneous application of crosslinking and ψ-analysis for examining potential transition state heterogeneity in globular proteins.
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Affiliation(s)
- Ali T Shandiz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
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28
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Mills BM, Chong LT. Molecular simulations of mutually exclusive folding in a two-domain protein switch. Biophys J 2011; 100:756-764. [PMID: 21281591 DOI: 10.1016/j.bpj.2010.12.3710] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 12/13/2010] [Accepted: 12/17/2010] [Indexed: 01/11/2023] Open
Abstract
A major challenge with testing designs of protein conformational switches is the need for experimental probes that can independently monitor their individual protein domains. One way to circumvent this issue is to use a molecular simulation approach in which each domain can be directly observed. Here we report what we believe to be the first molecular simulations of mutually exclusive folding in an engineered two-domain protein switch, providing a direct view of how folding of one protein drives unfolding of the other in a barnase-ubiquitin fusion protein. These simulations successfully capture the experimental effects of interdomain linker length and ligand binding on the extent of unfolding in the less stable domain. In addition, the effect of linker length on the potential for oligomerization, which eliminates switch activity, is in qualitative agreement with analytical ultracentrifugation experiments. We also perform what we believe to be the first study of protein unfolding via progressive localized compression. Finally, we are able to explore the kinetics of mutually exclusive folding by determining the effect of linker length on rates of unfolding and refolding of each protein domain. Our results demonstrate that molecular simulations can provide seemingly novel biological insights on the behavior of individual protein domains, thereby aiding in the rational design of bifunctional switches.
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Affiliation(s)
- Brandon M Mills
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania.
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29
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Pierre B, Xiong T, Hayles L, Guntaka VR, Kim JR. Stability of a guest protein depends on stability of a host protein in insertional fusion. Biotechnol Bioeng 2011; 108:1011-20. [DOI: 10.1002/bit.23039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/03/2010] [Accepted: 12/06/2010] [Indexed: 11/11/2022]
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30
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Sosnick TR, Barrick D. The folding of single domain proteins--have we reached a consensus? Curr Opin Struct Biol 2010; 21:12-24. [PMID: 21144739 DOI: 10.1016/j.sbi.2010.11.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/03/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
Abstract
Rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. These topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.
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Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
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31
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Kamneva OK, Liberles DA, Ward NL. Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method. Genome Biol Evol 2010; 2:870-86. [PMID: 21048002 PMCID: PMC3000692 DOI: 10.1093/gbe/evq071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Whole-genome scans for positive Darwinian selection are widely used to detect evolution of genome novelty. Most approaches are based on evaluation of nonsynonymous to synonymous substitution rate ratio across evolutionary lineages. These methods are sensitive to saturation of synonymous sites and thus cannot be used to study evolution of distantly related organisms. In contrast, indels occur less frequently than amino acid replacements, accumulate more slowly, and can be employed to characterize evolution of diverged organisms. As indels are also subject to the forces of natural selection, they can generate functional changes through positive selection. Here, we present a new computational approach to detect selective constraints on indel substitutions at the whole-genome level for distantly related organisms. Our method is based on ancestral sequence reconstruction, takes into account the varying susceptibility of different types of secondary structure to indels, and according to simulation studies is conservative. We applied this newly developed framework to characterize the evolution of organisms of the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) bacterial superphylum. The superphylum contains organisms with unique cell biology, physiology, and diverse lifestyles. It includes bacteria with simple cell organization and more complex eukaryote-like compartmentalization. Lifestyles range from free-living organisms to obligate pathogens. In this study, we conduct a whole-genome level analysis of indel substitutions specific to evolutionary lineages of the PVC superphylum and found that indels evolved under positive selection on up to 12% of gene tree branches. We also analyzed possible functional consequences for several case studies of predicted indel events.
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Affiliation(s)
| | | | - Naomi L. Ward
- Department of Molecular Biology, University of Wyoming
- Department of Botany, University of Wyoming
- Program in Ecology, University of Wyoming
- Corresponding author: E-mail:
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32
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Peng Q, Li H. Direct Observation of Tug-of-War during the Folding of a Mutually Exclusive Protein. J Am Chem Soc 2009; 131:13347-54. [DOI: 10.1021/ja903480j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qing Peng
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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33
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Kim CS, Pierre B, Ostermeier M, Looger LL, Kim JR. Enzyme stabilization by domain insertion into a thermophilic protein. Protein Eng Des Sel 2009; 22:615-23. [DOI: 10.1093/protein/gzp044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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34
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Zoldák G, Carstensen L, Scholz C, Schmid FX. Consequences of domain insertion on the stability and folding mechanism of a protein. J Mol Biol 2008; 386:1138-52. [PMID: 19136015 DOI: 10.1016/j.jmb.2008.12.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/17/2008] [Accepted: 12/18/2008] [Indexed: 11/30/2022]
Abstract
SlyD, the sensitive-to-lysis protein from Escherichia coli, consists of two domains. They are not arranged successively along the protein chain, but one domain, the "insert-in-flap" (IF) domain, is inserted internally as a guest into a surface loop of the host domain, which is a prolyl isomerase of the FK506 binding protein (FKBP) type. We used SlyD as a model to elucidate how such a domain insertion affects the stability and folding mechanism of the host and the guest domain. For these studies, the two-domain protein was compared with a single-domain variant SlyDDeltaIF, SlyD* without the chaperone domain (residues 1-69 and 130-165) in which the IF domain was removed and replaced by a short loop, as present in human FKBP12. Equilibrium unfolding and folding kinetics followed an apparent two-state mechanism in the absence and in the presence of the IF domain. The inserted domain decreased, however, the stability of the host domain in the transition region and decelerated its refolding reaction by about 10-fold. This originates from the interruption of the chain connectivity by the IF domain and its inherent instability. To monitor folding processes in this domain selectively, a Trp residue was introduced as fluorescent probe. Kinetic double-mixing experiments revealed that, in intact SlyD, the IF domain folds and unfolds about 1000-fold more rapidly than the FKBP domain, and that it is strongly stabilized when linked with the folded FKBP domain. The unfolding limbs of the kinetic chevrons of SlyD show a strong downward curvature. This deviation from linearity is not caused by a transition-state movement, as often assumed, but by the accumulation of a silent unfolding intermediate at high denaturant concentrations. In this kinetic intermediate, the FKBP domain is still folded, whereas the IF domain is already unfolded.
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Affiliation(s)
- Gabriel Zoldák
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
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35
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Lee BC, Chu TK, Dill KA, Zuckermann RN. Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc 2008; 130:8847-55. [PMID: 18597438 DOI: 10.1021/ja802125x] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the long-term goals in developing advanced biomaterials is to generate protein-like nanostructures and functions from a completely nonnatural polymer. Toward that end, we introduced a high-affinity zinc-binding function into a peptoid (N-substituted glycine polymer) two-helix bundle. Borrowing from well-understood zinc-binding motifs in proteins, thiol and imidazole moieties were positioned within the peptoid such that both helices must align in close proximity to form a binding site. We used fluorescence resonance energy transfer (FRET) reporter groups to measure the change of the distance between the two helical segments and to probe the binding of zinc. We systematically varied the position and number of zinc-binding residues, as well as the sequence and size of the loop that connects the two helical segments. We found that certain peptoid two-helix bundles bind zinc with nanomolar affinities and high selectivity compared to other divalent metal ions. Our work is a significant step toward generating biomimetic nanostructures with enzyme-like functions.
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Affiliation(s)
- Byoung-Chul Lee
- Biological Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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36
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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]
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37
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Abstract
We propose a new way to characterize protein folding transition states by (1) insertion of one or more residues into an unstructured protein loop, (2) measurement of the effect on protein folding kinetics and thermodynamics, and (3) analysis of the results in terms of a rate-equilibrium free energy relationship, alpha(Loop). alpha(Loop) reports on the fraction of molecules that form the perturbed loop in the transition state. Interpretation of the changes in equilibrium free energy using standard polymer theory can help detect residual structure in the unfolded state. We illustrate our approach with data for the model proteins CI2 and the alpha spectrin SH3 domain.
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38
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Weikl TR. Loop-closure principles in protein folding. Arch Biochem Biophys 2008; 469:67-75. [PMID: 17662688 DOI: 10.1016/j.abb.2007.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/20/2007] [Accepted: 06/22/2007] [Indexed: 10/23/2022]
Abstract
Simple theoretical concepts and models have been helpful to understand the folding rates and routes of single-domain proteins. As reviewed in this article, a physical principle that appears to underly these models is loop closure.
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Affiliation(s)
- Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, 14424 Potsdam, Germany.
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39
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Pradeep L, Udgaonkar JB. Diffusional Barrier in the Unfolding of a Small Protein. J Mol Biol 2007; 366:1016-28. [PMID: 17188296 DOI: 10.1016/j.jmb.2006.11.064] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 10/26/2006] [Accepted: 11/22/2006] [Indexed: 10/23/2022]
Abstract
To determine how the dynamics of the polypeptide chain in a protein molecule are coupled to the bulk solvent viscosity, the unfolding by urea of the small protein barstar was studied in the presence of two viscogens, xylose and glycerol. Thermodynamic studies of unfolding show that both viscogens stabilize barstar by a preferential hydration mechanism, and that viscogen and urea act independently on protein stability. Kinetic studies of unfolding show that while the rate-limiting conformational change during unfolding is dependent on the bulk solvent viscosity, eta, its rate does not show an inverse dependence on eta, as expected by Kramers' theory. Instead, the rate is found to be inversely proportional to an effective viscosity, eta + xi, where xi is an adjustable parameter which needs to be included in the rate equation. xi is found to have a value of -0.7 cP in xylose and -0.5 cP in glycerol, in the case of unfolding, at constant urea concentration as well as under isostability conditions. Hence, the unfolding protein chain does not experience the bulk solvent viscosity, but instead an effective solvent viscosity, which is lower than the bulk solvent viscosity by either 0.7 cP or 0.5 cP. A second important result is the validation of the isostability assumption, commonly used in protein folding studies but hitherto untested, according to which if a certain concentration of urea can nullify the effect of a certain concentration of viscogen on stability, then the same concentrations of urea and viscogen will also not perturb the free energy of activation of the unfolding of the protein.
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Affiliation(s)
- Lovy Pradeep
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
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40
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Mathonet P, Deherve J, Soumillion P, Fastrez J. Active TEM-1 beta-lactamase mutants with random peptides inserted in three contiguous surface loops. Protein Sci 2006; 15:2323-34. [PMID: 16963643 PMCID: PMC2242396 DOI: 10.1110/ps.062303606] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Engineering of alternative binding sites on the surface of an enzyme while preserving the enzymatic activity would offer new opportunities for controlling the activity by binding of non-natural ligands. Loops and turns are the natural substructures in which binding sites might be engineered with this purpose. We have genetically inserted random peptide sequences into three relatively rigid and contiguous loops of the TEM-1 beta-lactamase and assessed the tolerance to insertion by the percentage of active mutants. Our results indicate that tolerance to insertion could not be correlated to tolerance to mutagenesis. A turn between two beta-strands bordering the active site was observed to be tolerant to random mutagenesis but not to insertions. Two rigid loops comprising rather well-conserved amino acid residues tolerated insertions, although with some constraints. Insertions between the N-terminal helix and the first beta-strand generated active libraries if cysteine residues were included at both ends of the insert, suggesting the requirement for a stabilizing disulfide bridge. Random sequences were relatively well accommodated within the loop connecting the final beta-strand to the C-terminal helix, particularly if the wild-type residue was retained at one of the loops' end. This suggests two strategies for increasing the percentage of active mutants in insertion libraries. The amino acid distribution in the engineered loops was analyzed and found to be less biased against hydrophobic residues than in natural medium-sized loops. The combination of these activity-selected libraries generated a huge library containing active hybrid enzymes with all three loops modified.
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Affiliation(s)
- Pascale Mathonet
- Laboratoire de Biochimie Physique et des Biopolymères, Institut des Sciences de la Vie, Université catholique de Louvain, B1348 Louvain-la-Neuve, Belgium
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41
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Pandit AD, Jha A, Freed KF, Sosnick TR. Small Proteins Fold Through Transition States With Native-like Topologies. J Mol Biol 2006; 361:755-70. [PMID: 16876194 DOI: 10.1016/j.jmb.2006.06.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 06/12/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
The folding pathway of common-type acyl phosphatase (ctAcP) is characterized using psi-analysis, which identifies specific chain-chain contacts using bi-histidine (biHis) metal-ion binding sites. In the transition state ensemble (TSE), the majority of the protein is structured with a near-native topology, only lacking one beta-strand and an alpha-helix. psi-Values are zero or unity for all sites except one at the amino terminus of helix H2. This fractional psi-value remains unchanged when three metal ions of differing coordination geometries are used, indicating this end of the helix experiences microscopic heterogeneity through fraying in the TSE. Ubiquitin, the other globular protein characterized using psi-analysis, also exhibits a single consensus TSE structure. Hence, the TSE of both proteins have converged to a single configuration, albeit one that contains some fraying at the periphery. Models of the TSE of both proteins are created using all-atom Langevin dynamics simulations using distance constraints derived from the experimental psi-values. For both proteins, the relative contact order of the TS models is approximately 80% of the native value. This shared value viewed in the context of the known correlation between contact order and folding rates, suggests that other proteins will have a similarly high fraction of the native contact order. This constraint greatly limits the range of possible configurations at the rate-limiting step.
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Affiliation(s)
- Adarsh D Pandit
- Department of Biochemistry and Molecular Biology, and the Institute for Biophysical Dynamics, University of Chicago, 929 E. 57th St., Chicago, IL 60637, USA
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42
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Sosnick TR, Krantz BA, Dothager RS, Baxa M. Characterizing the Protein Folding Transition State Using ψ Analysis. Chem Rev 2006; 106:1862-76. [PMID: 16683758 DOI: 10.1021/cr040431q] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry, Institute for Biophysical Dynamics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.
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43
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Sagermann M, Baase WA, Matthews BW. Sequential reorganization of beta-sheet topology by insertion of a single strand. Protein Sci 2006; 15:1085-92. [PMID: 16597830 PMCID: PMC2242519 DOI: 10.1110/ps.052018006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Insertions, duplications, and deletions of sequence segments are thought to be major evolutionary mechanisms that increase the structural and functional diversity of proteins. Alternative splicing, for example, is an intracellular editing mechanism that is thought to generate isoforms for 30%-50% of all human genes. Whereas the inserted sequences usually display only minor structural rearrangements at the insertion site, recent observations indicate that they may also cause more dramatic structural displacements of adjacent structures. In the present study we test how artificially inserted sequences change the structure of the beta-sheet region in T4 lysozyme. Copies of two different beta-strands were inserted into two different loops of the beta-sheet, and the structures were determined. Not surprisingly, one insert "loops out" at its insertion site and forms a new small beta-hairpin structure. Unexpectedly, however, the second insertion leads to displacement of adjacent strands and a sequential reorganization of the beta-sheet topology. Even though the insertions were performed at two different sites, looping out occurred at the C-terminal end of the same beta-strand. Reasons as to why a non-native sequence would be recruited to replace that which occurs in the native protein are discussed. Our results illustrate how sequence insertions can facilitate protein evolution through both local and nonlocal changes in structure.
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Affiliation(s)
- Martin Sagermann
- Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA
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44
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Mello CC, Bradley CM, Tripp KW, Barrick D. Experimental characterization of the folding kinetics of the notch ankyrin domain. J Mol Biol 2005; 352:266-81. [PMID: 16095609 DOI: 10.1016/j.jmb.2005.07.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2004] [Revised: 06/01/2005] [Accepted: 07/11/2005] [Indexed: 10/25/2022]
Abstract
Proteins constructed from linear arrays of tandem repeats provide a simplified architecture for understanding protein folding. Here, we examine the folding kinetics of the ankyrin repeat domain from the Drosophila Notch receptor, which consists of six folded ankyrin modules and a seventh partly disordered N-terminal ankyrin repeat sequence. Both the refolding and unfolding kinetics are best described as a sum of two exponential phases. The slow, minor refolding phase is limited by prolyl isomerization in the denatured state (D). The minor unfolding phase, which appears as a lag during fluorescence-detected unfolding, is consistent with an on-pathway intermediate (I). This intermediate, although not directly detected during refolding, is shown to be populated by interrupted refolding experiments. When plotted against urea, the rate constants for the major unfolding and refolding phases define a single non-linear v-shaped chevron, as does the minor unfolding phase. These two chevrons, along with unfolding amplitudes, are well-fitted by a sequential three-state model, which yields rate constants for the individual steps in folding and unfolding. Based on these fitted parameters, the D to I step is rate-limiting, and closely matches the major observed refolding phase at low denaturant concentrations. I appears to be midway between N and D in folding free energy and denaturant sensitivity, but has Trp fluorescence properties close to N. Although the Notch ankyrin domain has a simple architecture, folding is slow, with the limiting refolding rate constant as much as seven orders of magnitude smaller than expected from topological predictions.
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Affiliation(s)
- Cecilia C Mello
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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45
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Wang L, Rivera EV, Benavides-Garcia MG, Nall BT. Loop Entropy and Cytochrome c Stability. J Mol Biol 2005; 353:719-29. [PMID: 16182309 DOI: 10.1016/j.jmb.2005.08.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 08/15/2005] [Accepted: 08/18/2005] [Indexed: 11/18/2022]
Abstract
The loop entropy model proposes that loop closure in a protein becomes entropically more costly as the length of the loop increases. A model protein, cytochrome c, is composed of four loops connecting five helices surrounding a heme-containing core. To test the loop entropy model a series of mutant proteins are constructed with (Gly)n or (Thr)n segments (n = 4-20) inserted between Gly23 and Gly24 of omega loop A of a pseudo wild-type reference protein. Scanning calorimetry shows that protein stability decreases as n increases in the (Gly)n or (Thr)n segment. The dependence of stability on loop length is analyzed with the loop entropy model. Fitting to the model gives a quantitative description of stability differences for the mutant proteins, but with a smaller power-dependence of the probability of loop closure (c-value) than expected from polymer theory. A possible explanation for the discrepancy is that thermodynamically unfavorable loop entropy is partially offset by interactions between the inserted homopolymer and flanking heteropolymer portions of the unfolded protein. The interactions may involve molecular crowding that favors coalescence of the heteropolymer at the insert site and thus closure of the homopolymer loops, possibly as an aspect of the folding code. This may allow use of loop insert mutants to assess the strength of the heteropolymer-encoded folding signals that facilitate loop closure at the insert site.
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Affiliation(s)
- Liping Wang
- Center for Biomolecular Structure Analysis, Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
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46
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López-Llano J, Maldonado S, Jain S, Lostao A, Godoy-Ruiz R, Sanchez-Ruiz JM, Cortijo M, Fernández-Recio J, Sancho J. The Long and Short Flavodoxins. J Biol Chem 2004; 279:47184-91. [PMID: 15317817 DOI: 10.1074/jbc.m405791200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Flavodoxins are classified in two groups according to the presence or absence of a approximately 20-residue loop of unknown function. In the accompanying paper (36), we have shown that the differentiating loop from the long-chain Anabaena PCC 7119 flavodoxin is a peripheral structural element that can be removed without preventing the proper folding of the apoprotein. Here we investigate the role played by the loop in the stability and folding mechanism of flavodoxin by comparing the equilibrium and kinetic behavior of the full-length protein with that of loop-lacking, shortened variants. We show that, when the loop is removed, the three-state equilibrium thermal unfolding of apoflavodoxin becomes two-state. Thus, the loop is responsible for the complexity shown by long-chain apoflavodoxins toward thermal denaturation. As for the folding reaction, both shortened and wild type apoflavodoxins display three-state behavior but their folding mechanisms clearly differ. Whereas the full-length protein populates an essentially off-pathway transient intermediate, the additional state observed in the folding of the shortened variant analyzed seems to be simply an alternative native conformation. This finding suggests that the long loop may also be responsible for the accumulation of the kinetic intermediate observed in the full-length protein. Most revealing, however, is that the influence of the loop on the overall conformational stability of apoflavodoxin is quite low and the natively folded shortened variant Delta(120-139) is almost as stable as the wild type protein. The fact that the loop, which is not required for a proper folding of the polypeptide, does not even play a significant role in increasing the conformational stability of the protein supports our proposal (36) that the differentiating loop of long-chain flavodoxins may be related to a recognition function, rather than serving a structural purpose.
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Affiliation(s)
- Jon López-Llano
- Biocomputation and Complex Systems Physics Institute, Zaragoza University, Zaragoza, Spain
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47
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Knappenberger JA, Kraemer-Pecore CM, Lecomte JTJ. Insertion of the cytochrome b5 heme-binding loop into an SH3 domain. Effects on structure and stability, and clues about the cytochrome's architecture. Protein Sci 2004; 13:2899-908. [PMID: 15459337 PMCID: PMC2286592 DOI: 10.1110/ps.04902704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Under native conditions, apocytochrome b(5) exhibits a stable core and a disordered heme-binding region that refolds upon association with the cofactor. The termini of this flexible region are in close proximity, suggesting that loop closure may contribute to the thermodynamic properties of the apocytochrome. A chimeric protein containing 43 residues encompassing the cytochrome loop was constructed using the cyanobacterial photosystem I accessory protein E (PsaE) from Synechococcus sp. PCC 7002 as a structured scaffold. PsaE has the topology of an SH3 domain, and the insertion was engineered to replace its 14-residue CD loop. NMR and optical spectroscopies showed that the hybrid protein (named EbE1) was folded under native conditions and that it retained the characteristics of an SH3 domain. NMR spectroscopy revealed that structural and dynamic differences were confined near the site of loop insertion. Variable-temperature 1D NMR spectra of EbE1 confirmed the presence of a kinetic unfolding barrier. Thermal and chemical denaturations of PsaE and EbE1 demonstrated cooperative, two-state transitions; the stability of the PsaE scaffold was found only moderately compromised by the insertion, with a DeltaT(m) of 8.3 degrees C, a DeltaC(m) of 1.5 M urea, and a DeltaDeltaG degrees of 4.2 kJ/mole. The data implied that the penalty for constraining the ends of the inserted region was lower than the approximately 6.4 kJ/mole calculated for a self-avoiding chain. Extrapolation of these results to cytochrome b(5) suggested that the intrinsic stability of the folded portion of the apoprotein reflected only a small detrimental contribution from the large heme-binding domain.
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Affiliation(s)
- Jane A Knappenberger
- Chemistry Department, The Pennsylvania State University, 152 Davey Laboratory, University Park, PA 16802, USA
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48
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Finke JM, Cheung MS, Onuchic JN. A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys J 2004; 87:1900-18. [PMID: 15345567 PMCID: PMC1304594 DOI: 10.1529/biophysj.104.041533] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 05/17/2004] [Indexed: 11/18/2022] Open
Abstract
Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (C(alpha)C(beta)) of CI2 is developed with a structurally based potential and captures many of the folding properties of CI2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the CI2 "host" model and the polyglutamine is modeled to match the resultant change in CI2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in CI2 thermodynamic stability has 1), a beta-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the CI2 host Go-contacts. When free-energy differences in the CI2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.
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Affiliation(s)
- John M Finke
- The Center for Theoretical Biological Physics and the Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
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Abstract
Understanding the sequence determinants of protein structure, stability and folding is critical for understanding how natural proteins have evolved and how proteins can be engineered to perform novel functions. The complexity of the protein folding problem requires the ability to search large volumes of sequence space for proteins with specific structural or functional characteristics. Here we describe our efforts to identify novel proteins using a phage-display selection strategy from a 'mini-exon' shuffling library generated from the yeast genome and from completely random sequence libraries, and compare the results to recent successes in generating novel proteins using in silico protein design.
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Affiliation(s)
- Alexander L Watters
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
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Bai Y, Zhou H, Zhou Y. Critical nucleation size in the folding of small apparently two-state proteins. Protein Sci 2004; 13:1173-81. [PMID: 15075405 PMCID: PMC2286761 DOI: 10.1110/ps.03587604] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For apparently two-state proteins, we found that the size (number of folded residues) of a transition state is mostly encoded by the topology, defined by total contact distance (TCD) of the native state, and correlates with its folding rate. This is demonstrated by using a simple procedure to reduce the native structures of the 41 two-state proteins with native TCD as a constraint, and is further supported by analyzing the results of eight proteins from protein engineering studies. These results support the hypothesis that the major rate-limiting process in the folding of small apparently two-state proteins is the search for a critical number of residues with the topology close to that of the native state.
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Affiliation(s)
- Yawen Bai
- Laboratory of Biochemistry, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA.
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