1
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Cho MK, Chong SH, Shin S, Ham S. Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain. J Phys Chem B 2021; 125:7108-7116. [PMID: 34165991 DOI: 10.1021/acs.jpcb.1c01725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The native structure of a protein is stabilized by a number of interactions such as main-chain hydrogen bonds and side-chain hydrophobic contacts. However, it has been challenging to determine how these interactions contribute to protein stability at single amino acid resolution. Here, we quantified site-specific thermodynamic stability at the molecular level to extend our understanding of the stabilizing forces in protein folding. We derived the free energy components of individual amino acid residues separately for the folding of the human Pin WW domain based on simulated structures. A further decomposition of the thermodynamic properties into contributions from backbone and side-chain groups enabled us to identify the critical residues in the secondary structure and hydrophobic core formation, without introducing physical modifications to the system as in site-directed mutagenesis methods. By relating the structural and thermodynamic changes upon folding for each residue, we find that the simultaneous formation of the backbone hydrogen bonds and side-chain contacts cooperatively stabilizes the folded structure. The identification of stabilizing interactions in a folding protein at atomic resolution will provide molecular insights into understanding the origin of the protein structure and into engineering a more stable protein.
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Affiliation(s)
- Myung Keun Cho
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea.,Department of Chemistry, College of Natural Sciences, Seoul National University, Gwanak-ro 1, Gwanak-ku, Seoul 08826, Korea
| | - Song-Ho Chong
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Seokmin Shin
- Department of Chemistry, College of Natural Sciences, Seoul National University, Gwanak-ro 1, Gwanak-ku, Seoul 08826, Korea
| | - Sihyun Ham
- Department of Chemistry, the Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-ku, Seoul 04310, Korea
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2
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Jia X, Yang Y, Liu Y, Niu W, Li YQ, Zhao M, Mu Y, Li W. Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping. NANOSCALE ADVANCES 2020; 2:4539-4546. [PMID: 36132907 PMCID: PMC9417744 DOI: 10.1039/d0na00365d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/25/2020] [Indexed: 06/16/2023]
Abstract
In recent years, nanomaterials have attracted considerable research attention for biological and medical related applications due to their well-recognized physical and chemical properties. However, the deep understanding of the binding process at the protein-nanomaterial interface is essential to solve the concern of nano-toxicity. Here, we study the interactions between the recently reported graphenic nano-sheets, BC3 and C3N, and a prototypical protein (YAP65WW domain) via atomistic molecular dynamics simulations. Our simulations reveal that elemental doping is an effective way to tune the binding characteristics of YAP65WW with two nanomaterials. While YAP65WW can be attracted by two nanomaterials, the BC3 sheet is less able to disrupt the protein structure than C3N. From the energy point of view, this is because protein residues demonstrate a binding preference with the trend from electron rich nitrogen to electron deficient boron. Structural analyses of the bio-nano interface revealed the formation of an ordered water shell on the BC3 surface, which was compatible to the crystal pattern of BC3. When a protein binds with BC3, these interfacial water molecules protect the protein from being disrupted. We suggest that elemental doping is efficient to produce fruitful biological-effects of graphenic nanomaterials, which make it a prospective solution for the future design and fabrication of advanced nanomaterials with desired function.
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Affiliation(s)
- Xiao Jia
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yang Liu
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Weihua Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 China
| | - Yong-Qiang Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Mingwen Zhao
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University 637551 Singapore
| | - Weifeng Li
- School of Physics, State Key Laboratory of Crystal Materials, Shandong University Jinan Shandong 250100 China
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3
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Legname G, Virgilio T, Bistaffa E, De Luca CMG, Catania M, Zago P, Isopi E, Campagnani I, Tagliavini F, Giaccone G, Moda F. Effects of peptidyl-prolyl isomerase 1 depletion in animal models of prion diseases. Prion 2018; 12:127-137. [PMID: 29676205 DOI: 10.1080/19336896.2018.1464367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Pin1 is a peptidyl-prolyl isomerase that induces the cis-trans conversion of specific Ser/Thr-Pro peptide bonds in phosphorylated proteins, leading to conformational changes through which Pin1 regulates protein stability and activity. Since down-regulation of Pin1 has been described in several neurodegenerative disorders, including Alzheimer's Disease (AD), Parkinson's Disease (PD) and Huntington's Disease (HD), we investigated its potential role in prion diseases. Animals generated on wild-type (Pin1+/+), hemizygous (Pin1+/-) or knock-out (Pin1-/-) background for Pin1 were experimentally infected with RML prions. The study indicates that, neither the total depletion nor reduced levels of Pin1 significantly altered the clinical and neuropathological features of the disease.
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Affiliation(s)
- Giuseppe Legname
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy.,c ELETTRA Laboratory , Sincrotrone Trieste S.C.p.A , Basovizza, Trieste , Italy
| | - Tommaso Virgilio
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy.,d Institute for Research in Biomedicine, Università della Svizzera Italiana , Bellinzona , Switzerland
| | - Edoardo Bistaffa
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy.,b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Chiara Maria Giulia De Luca
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Marcella Catania
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Paola Zago
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy
| | - Elisa Isopi
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy
| | - Ilaria Campagnani
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Fabrizio Tagliavini
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Giorgio Giaccone
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Fabio Moda
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
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4
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Qiao X, Liu Y, Luo L, Chen L, Zhao C, Ai X. Effects of naturally occurring charged mutations on the structure, stability, and binding of the Pin1 WW domain. Biochem Biophys Res Commun 2017; 487:470-476. [PMID: 28431929 DOI: 10.1016/j.bbrc.2017.04.093] [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: 04/08/2017] [Accepted: 04/18/2017] [Indexed: 11/26/2022]
Abstract
Pin1 is a peptidyl-prolyl cis-trans isomerase, whose WW domain specifically recognizes the pSer/Thr-Pro motif. Pin1 is involved in multiple phosphorylation events that regulate the activities of various substrates, and Pin1 deregulation has been reported in various diseases, including cancer and Alzheimer's disease. The WW domain of Pin1 has been used as a small model protein to investigate the folding mechanisms of the β-sheet structure by studying the effect of mutations or its naturally occurring variants. However, only a few studies have investigated the structure and binding of Pin1 WW mutants. In the present work, two naturally occurring Pin1 WW variants, namely, G20D and S16R, derived from the cynomolgus monkey and African green monkey, respectively, were selected to investigate the influence of charge mutation on the structure, stability, and binding properties of the Pin1 WW domain. Analysis using a combination of nuclear magnetic resonance (NMR) and chemical shift-based calculations revealed that the G20D and S16R mutants had high structural similarity to the wild-type Pin1 WW domain. However, the presence of a charge mutation significantly decreased the stability of the Pin1 WW domain. Both the wild-type and G20D forms of the Pin1 WW domain utilized a three-site mode to bind to a phosphorylated Tau peptide, pT231, whereas the S16R mutant binds to the pT231 peptide either in a non-specific manner or through a totally different binding mechanism. Correspondingly, the wild-type and two mutant Pin1 WW domains showed different binding affinities to the Tau phosphopeptide. Considering that the WW domain participates in the catalytic activity of the Pin1 isomerase, our study represents a novel approach for studying Pin1 function through the analysis of its naturally occurring mutants.
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Affiliation(s)
- Xiaoya Qiao
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China; Division of Energy Research Resources, National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Ying Liu
- Division of Virology & Immunology, National Center for AIDS/STD Control and Prevention, Beijing 102206, PR China
| | - Liting Luo
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Lei Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Caixian Zhao
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China.
| | - Xuanjun Ai
- Division of Energy Research Resources, National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
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5
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Hsu CH, Park S, Mortenson DE, Foley BL, Wang X, Woods RJ, Case DA, Powers ET, Wong CH, Dyson HJ, Kelly JW. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc 2016; 138:7636-48. [PMID: 27249581 DOI: 10.1021/jacs.6b02879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate-aromatic interaction. Our data demonstrate that the carbohydrate-aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar-aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes.
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Affiliation(s)
- Che-Hsiung Hsu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Sangho Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - David E Mortenson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - B Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
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6
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Davis CM, Dyer RB. The Role of Electrostatic Interactions in Folding of β-Proteins. J Am Chem Soc 2016; 138:1456-64. [PMID: 26750867 DOI: 10.1021/jacs.5b13201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Atomic-level molecular dynamic simulations are capable of fully folding structurally diverse proteins; however, they are limited in their ability to accurately represent electrostatic interactions. Here we have experimentally tested the role of charged residues on stability and folding kinetics of one of the most widely simulated β-proteins, the WW domain. The folding of wild type Pin1 WW domain, which has two positively charged residues in the first turn, was compared to the fast folding mutant FiP35 Pin1, which introduces a negative charge into the first turn. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the amide I region. The relaxation dynamics of the peptide backbone, β-sheets and β-turns, and negatively charged aspartic acid side chain of FiP35 were measured independently by probing the corresponding bands assigned in the amide I region. Folding is initiated in the turns and the β-sheets form last. While the global folding mechanism is in good agreement with simulation predictions, we observe changes in the protonation state of aspartic acid during folding that have not been captured by simulation methods. The protonation state of aspartic acid is coupled to protein folding; the apparent pKa of aspartic acid in the folded protein is 6.4. The dynamics of the aspartic acid follow the dynamics of the intermediate phase, supporting assignment of this phase to formation of the first hairpin. These results demonstrate the importance of electrostatic interactions in turn stability and formation of extended β-sheet structures.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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7
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The structural and functional role of the three tryptophan residues in Pin1. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 146:58-67. [DOI: 10.1016/j.jphotobiol.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/25/2015] [Accepted: 03/12/2015] [Indexed: 11/23/2022]
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8
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Lawrence PB, Gavrilov Y, Matthews SS, Langlois MI, Shental-Bechor D, Greenblatt HM, Pandey BK, Smith MS, Paxman R, Torgerson CD, Merrell JP, Ritz CC, Prigozhin MB, Levy Y, Price JL. Criteria for Selecting PEGylation Sites on Proteins for Higher Thermodynamic and Proteolytic Stability. J Am Chem Soc 2014; 136:17547-60. [DOI: 10.1021/ja5095183] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Paul B. Lawrence
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yulian Gavrilov
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sam S. Matthews
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Minnie I. Langlois
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dalit Shental-Bechor
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M. Greenblatt
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Brijesh K. Pandey
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mason S. Smith
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan Paxman
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Chad D. Torgerson
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jacob P. Merrell
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Cameron C. Ritz
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Maxim B. Prigozhin
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yaakov Levy
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joshua L. Price
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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9
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Focusing on the structure and the function of Pin1: New insights into the opposite effects of fever on cancers and Alzheimer’s disease. Med Hypotheses 2013; 81:282-4. [DOI: 10.1016/j.mehy.2013.04.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 04/11/2013] [Accepted: 04/16/2013] [Indexed: 12/22/2022]
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10
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Price JL, Culyba EK, Chen W, Murray AN, Hanson SR, Wong CH, Powers ET, Kelly JW. N-glycosylation of enhanced aromatic sequons to increase glycoprotein stability. Biopolymers 2012; 98:195-211. [PMID: 22782562 PMCID: PMC3539202 DOI: 10.1002/bip.22030] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/17/2012] [Accepted: 01/26/2012] [Indexed: 11/12/2022]
Abstract
N-glycosylation can increase the rate of protein folding, enhance thermodynamic stability, and slow protein unfolding; however, the molecular basis for these effects is incompletely understood. Without clear engineering guidelines, attempts to use N-glycosylation as an approach for stabilizing proteins have resulted in unpredictable energetic consequences. Here, we review the recent development of three "enhanced aromatic sequons," which appear to facilitate stabilizing native-state interactions between Phe, Asn-GlcNAc and Thr when placed in an appropriate reverse turn context. It has proven to be straightforward to engineer a stabilizing enhanced aromatic sequon into glycosylation-naïve proteins that have not evolved to optimize specific protein-carbohydrate interactions. Incorporating these enhanced aromatic sequons into appropriate reverse turn types within proteins should enhance the well-known pharmacokinetic benefits of N-glycosylation-based stabilization by lowering the population of protease-susceptible unfolded and aggregation-prone misfolded states, thereby making such proteins more useful in research and pharmaceutical applications.
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Affiliation(s)
- Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Elizabeth K. Culyba
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Wentao Chen
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Amber N. Murray
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Sarah R. Hanson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
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11
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Price JL, Shental-Bechor D, Dhar A, Turner MJ, Powers ET, Gruebele M, Levy Y, Kelly JW. Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics. J Am Chem Soc 2010; 132:15359-67. [PMID: 20936810 PMCID: PMC2965790 DOI: 10.1021/ja106896t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Asparagine glycosylation is one of the most common and important post-translational modifications of proteins in eukaryotic cells. N-glycosylation occurs when a triantennary glycan precursor is transferred en bloc to a nascent polypeptide (harboring the N-X-T/S sequon) as the peptide is cotranslationally translocated into the endoplasmic reticulum (ER). In addition to facilitating binding interactions with components of the ER proteostasis network, N-glycans can also have intrinsic effects on protein folding by directly altering the folding energy landscape. Previous work from our laboratories (Hanson et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 109, 3131-3136; Shental-Bechor, D.; Levy, Y. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261) suggested that the three sugar residues closest to the protein are sufficient for accelerating protein folding and stabilizing the resulting structure in vitro; even a monosaccharide can have a dramatic effect. The highly conserved nature of these three proximal sugars in N-glycans led us to speculate that introducing an N-glycosylation site into a protein that is not normally glycosylated would stabilize the protein and increase its folding rate in a manner that does not depend on the presence of specific stabilizing protein-saccharide interactions. Here, we test this hypothesis experimentally and computationally by incorporating an N-linked GlcNAc residue at various positions within the Pin WW domain, a small β-sheet-rich protein. The results show that an increased folding rate and enhanced thermodynamic stability are not general, context-independent consequences of N-glycosylation. Comparison between computational predictions and experimental observations suggests that generic glycan-based excluded volume effects are responsible for the destabilizing effect of glycosylation at highly structured positions. However, this reasoning does not adequately explain the observed destabilizing effect of glycosylation within flexible loops. Our data are consistent with the hypothesis that specific, evolved protein-glycan contacts must also play an important role in mediating the beneficial energetic effects on protein folding that glycosylation can confer.
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Affiliation(s)
- Joshua L. Price
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Dalit Shental-Bechor
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
| | - Apratim Dhar
- Center for Biophysics and Computational Biology and Departments of Chemistry and Physics, University of Illinois, Urbana, Illinois 61801
| | - Maurice J. Turner
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Evan T. Powers
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Martin Gruebele
- Center for Biophysics and Computational Biology and Departments of Chemistry and Physics, University of Illinois, Urbana, Illinois 61801
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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12
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Jäger M, Dendle M, Kelly JW. Sequence determinants of thermodynamic stability in a WW domain--an all-beta-sheet protein. Protein Sci 2009; 18:1806-13. [PMID: 19565466 DOI: 10.1002/pro.172] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The stabilities of 66 sequence variants of the human Pin1 WW domain have been determined by equilibrium thermal denaturation experiments. All 34 residues composing the hPin1 WW three-stranded beta-sheet structure could be replaced one at a time with at least one different natural or non-natural amino acid residue without leading to an unfolded protein. Alanine substitutions at only four positions within the hPin1 WW domain lead to a partially or completely unfolded protein-in the absence of a physiological ligand. The side chains of these four residues form a conserved, partially solvent-inaccessible, continuous hydrophobic minicore comprising the N- and C-termini. Ala mutations at five other residues, three of which constitute the ligand binding patch on the concave side of the beta-sheet, significantly destabilize the hPin1 WW domain without leading to an unfolded protein. The remaining mutations affect protein stability only slightly, suggesting that only a small subset of side chain interactions within the hPin1 WW domain are mandatory for acquiring and maintaining a stable, cooperatively folded beta-sheet structure.
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Affiliation(s)
- Marcus Jäger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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13
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Abstract
Beta-turns are common conformations that enable proteins to adopt globular structures, and their formation is often rate limiting for folding. Beta-turn mimics, molecules that replace the i + 1 and i + 2 amino acid residues of a beta-turn, are envisioned to act as folding nucleators by preorganizing the pendant polypeptide chains, thereby lowering the activation barrier for beta-sheet formation. However, the crucial kinetic experiments to demonstrate that beta-turn mimics can act as strong nucleators in the context of a cooperatively folding protein have not been reported. We have incorporated 6 beta-turn mimics simulating varied beta-turn types in place of 2 residues in an engineered beta-turn 1 or beta-bulge turn 1 of the Pin 1 WW domain, a three-stranded beta-sheet protein. We present 2 lines of kinetic evidence that the inclusion of beta-turn mimics alters beta-sheet folding rates, enabling us to classify beta-turn mimics into 3 categories: those that are weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong nucleators accelerate folding relative to WW domains incorporating all alpha-amino acid sequences. A solution NMR structure reveals that the native Pin WW beta-sheet structure is retained upon incorporating a strong E-olefin nucleator. These beta-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other beta-turn mimics.
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14
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Jager M, Deechongkit S, Koepf EK, Nguyen H, Gao J, Powers ET, Gruebele M, Kelly JW. Understanding the mechanism of beta-sheet folding from a chemical and biological perspective. Biopolymers 2009; 90:751-8. [PMID: 18844292 DOI: 10.1002/bip.21101] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Perturbing the structure of the Pin1 WW domain, a 34-residue protein comprised of three beta-strands and two intervening loops has provided significant insight into the structural and energetic basis of beta-sheet folding. We will review our current perspective on how structure acquisition is influenced by the sequence, which determines local conformational propensities and mediates the hydrophobic effect, hydrogen bonding, and analogous intramolecular interactions. We have utilized both traditional site-directed mutagenesis and backbone mutagenesis approaches to alter the primary structure of this beta-sheet protein. Traditional site-directed mutagenesis experiments are excellent for altering side-chain structure, whereas amide-to-ester backbone mutagenesis experiments modify backbone-backbone hydrogen bonding capacity. The transition state structure associated with the folding of the Pin1 WW domain features a partially H-bonded, near-native reverse turn secondary structure in loop 1 that has little influence on thermodynamic stability. The thermodynamic stability of the Pin1 WW domain is largely determined by the formation of a small hydrophobic core and by the formation of desolvated backbone-backbone H-bonds enveloped by this hydrophobic core. Loop 1 engineering to the consensus five-residue beta-bulge-turn found in most WW domains or a four-residue beta-turn found in most beta-hairpins accelerates folding substantially relative to the six-residue turn found in the wild type Pin1 WW domain. Furthermore, the more efficient five- and four-residue reverse turns now contribute to the stability of the three-stranded beta-sheet. These insights have allowed the design of Pin1 WW domains that fold at rates that approach the theoretical speed limit of folding.
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Affiliation(s)
- Marcus Jager
- Department of Chemistry, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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15
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Kier BL, Andersen NH. Probing the lower size limit for protein-like fold stability: ten-residue microproteins with specific, rigid structures in water. J Am Chem Soc 2008; 130:14675-83. [PMID: 18842046 DOI: 10.1021/ja804656h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutational optimization of two long-range interactions first observed in Ac-WINGKWT-NH2, (a) bifurcated H-bonding involving the threonine amide H(N) and side chain OH and the N-terminal acetyl carbonyl and (b) an H-bond between the entgegen-H(N) of the C-terminal amide and the indole ring of Trp6 that stabilizes a face-to-edge indole/indole interaction between Trp1 and Trp6, has afforded < or = 10 residue systems that yield a remarkably stable fold in water. Optimization was achieved by designing a hydrophobic cluster that sequesters these H-bonds from solvent exposure. The structures and extent of amide H/D exchange protection for CH3CH2CO-WI pGXWTGPS (p = D-Pro, X = Leu or Ile) were determined. These two systems are greater than 94% folded at 298 K (97.5% at 280 K) with melting temperatures > 75 degrees C. The fold appears to display minimal fluxionality; a well-converged NMR structure rationalizes all of the large structuring shifts observed, and we suggest that these designed constructs can be viewed as microproteins.
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Affiliation(s)
- Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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16
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Luo Z, Ding J, Zhou Y. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. J Chem Phys 2008; 128:225103. [PMID: 18554060 DOI: 10.1063/1.2936832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper examines the folding mechanism of an individual beta-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel beta-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single beta-hairpin in literature is confirmed to be useful in describing beta-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, beta1-beta2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of beta2-beta3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.
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Affiliation(s)
- Zhonglin Luo
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, People's Republic of China
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17
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Ohnishi S, Tochio N, Tomizawa T, Akasaka R, Harada T, Seki E, Sato M, Watanabe S, Fujikura Y, Koshiba S, Terada T, Shirouzu M, Tanaka A, Kigawa T, Yokoyama S. Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily. Protein Sci 2008; 17:1531-41. [PMID: 18562638 DOI: 10.1110/ps.035329.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain.
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Affiliation(s)
- Satoshi Ohnishi
- Systems and Structural Biology Center, RIKEN, Tsurumi, Yokohama 230-0045, Japan
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18
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Torrent J, Marchal S, Ribó M, Vilanova M, Georges C, Dupont Y, Lange R. Distinct unfolding and refolding pathways of ribonuclease a revealed by heating and cooling temperature jumps. Biophys J 2008; 94:4056-65. [PMID: 18234832 PMCID: PMC2367170 DOI: 10.1529/biophysj.107.123893] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 12/21/2007] [Indexed: 11/18/2022] Open
Abstract
Heating and cooling temperature jumps (T-jumps) were performed using a newly developed technique to trigger unfolding and refolding of wild-type ribonuclease A and a tryptophan-containing variant (Y115W). From the linear Arrhenius plots of the microscopic folding and unfolding rate constants, activation enthalpy (DeltaH(#)), and activation entropy (DeltaS(#)) were determined to characterize the kinetic transition states (TS) for the unfolding and refolding reactions. The single TS of the wild-type protein was split into three for the Y115W variant. Two of these transition states, TS1 and TS2, characterize a slow kinetic phase, and one, TS3, a fast phase. Heating T-jumps induced protein unfolding via TS2 and TS3; cooling T-jumps induced refolding via TS1 and TS3. The observed speed of the fast phase increased at lower temperature, due to a strongly negative DeltaH(#) of the folding-rate constant. The results are consistent with a path-dependent protein folding/unfolding mechanism. TS1 and TS2 are likely to reflect X-Pro(114) isomerization in the folded and unfolded protein, respectively, and TS3 the local conformational change of the beta-hairpin comprising Trp(115). A very fast protein folding/unfolding phase appears to precede both processes. The path dependence of the observed kinetics is suggestive of a rugged energy protein folding funnel.
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Affiliation(s)
- Joan Torrent
- Université Montpellier 2, UMR-S710, and INSERM Unit 710, Montpellier, France
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19
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Ng CA, Kato Y, Tanokura M, Brownlee RTC. Structural characterisation of PinA WW domain and a comparison with other group IV WW domains, Pin1 and Ess1. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1208-14. [PMID: 18503784 DOI: 10.1016/j.bbapap.2008.04.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 04/17/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
The NMR solution structure of the PinA WW domain from Aspergillus nidulans is presented. The backbone of the PinA WW domain is composed of a triple-stranded anti-parallel beta-sheet and an alpha-helix similar to Ess1 and Pin1 without the alpha-helix linker. Large RMS deviations in Loop I were observed both from the NMR structures and molecular dynamics simulation suggest that the Loop I of PinA WW domain is flexible and solvent accessible, thus enabling it to bind the pS/pT-P motif. The WW domain in this structure are stabilised by a hydrophobic core. It is shown that the linker flexibility of PinA is restricted because of an alpha-helical structure in the linker region. The combination of NMR structural data and detailed Molecular Dynamics simulations enables a comprehensive structural and dynamic understanding of this protein.
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Affiliation(s)
- Chai Ann Ng
- Department of Chemistry, La Trobe University, VIC 3086, Australia
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