1
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Nandi S, Sarkar R, Jaiswar A, Roy S, Haldar D. Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions. ACS OMEGA 2022; 7:17245-17252. [PMID: 35647431 PMCID: PMC9134230 DOI: 10.1021/acsomega.2c01168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure. However, hybrid tripeptides with an N-terminal Boc-Trp-Aib corner residue and C-terminal aromatic ω-amino acids fold into the hairpin conformation with a central β-turn/open-turn that is reinforced by a C-H···π interaction. The CCDC database analysis further confirms that this C-H···π stabilized hairpin motif is general for Boc-protected tripeptides containing Aib in the middle and aromatic functionality at the C-terminus. The different α-amino acids like Leu/Ala/Phe/Pro/Ser at the N-terminus have a minor influence on the C-H···π interaction and stabilities of the folded structures in solid-state. However, the hybrid peptides exhibit different degrees of conformational heterogeneity both in the solid and solution phase, which is common for this kind of flexible small molecule. Conformational heterogeneity in the solution phase including the C-H···π stabilized β-hairpin structures are characterized by the molecular dynamics (MD) simulations explaining their plausible origin at an atomistic level.
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Affiliation(s)
- Sujay
Kumar Nandi
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Raju Sarkar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Susmita Roy
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Debasish Haldar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
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2
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Sun XY, Zhong Y, Li YH, Miller DP, Buttan S, Wu XX, Zhang Y, Tang Q, Tan HW, Zhu J, Liu R, Zurek E, Lu ZL, Gong B. Reliable folding of hybrid tetrapeptides into short β-hairpins. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Zhong Y, Tang Q, Miller DP, Zurek E, Liu R, Lu ZL, Gong B. Major Factors for the Persistent Folding of Hybrid α, β, γ-Hybrid Peptides Into Hairpins. Front Chem 2020; 8:530083. [PMID: 33134269 PMCID: PMC7550740 DOI: 10.3389/fchem.2020.530083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
Factors responsible for the persistent adoption of hairpin conformations by hybrid oligopeptides, each having a central β/α dipeptide segment flanked by aromatic γ-amino acid (γAr) residues, are probed. Our recent studies revealed that tetrapeptide 1 and 2, having central dipeptide segments consisting of β-alanine (β-Ala) and glycine (Gly), and L-β-homophenylalanine (L-β-homoPhe) and Gly residues, respectively, that are flanked by γAr residues, fold into well-defined, expanded β-turns with doubly H-bonded γAr residues. Replacing the γAr residues of 1 and 2 with L-Val and L-Leu residues results in tetrapetides 1 ' and 2 ' that fail to fold into defined conformations, which confirms the decisive role played by the H-bonded γAr residues in the promoting folding of 1 and 2. Attaching L-Val and L-Leu residues to the termini of 1 affords hexapeptide 1a. With an additional H-bond between its L-Val and L-Leu residues, peptide 1a folds into a hairpin with higher stability than that of 1, indicating that the expanded β-turn can nucleate and stabilize β-hairpin with longer β-strands. Attaching L-Val and L-Leu residues to the termini of 2 affords hexapeptide 2a. Substituting the L-β-homoPhe residue of 2a with a D-β-homoPhe residue gives hexapeptide 2b. Surprisingly, hexapeptide 2a fold into a hairpin showing the similar stability as those of tetrapeptides 1 and 2. Hexapeptide 2b, with its combination of a D-β-homoPhe residue and the L-Val/L-Leu pair, fold into a hairpin that is significantly more stable than the other hybrid peptides, demonstrating that a combination of hetero-chirality between the β-amino acid residue of the dipeptide loop and the α-amino acid residues of the β-strands enhances the stability of the resultant β-hairpin.
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Affiliation(s)
- Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Quan Tang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
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4
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Tang Q, Zhong Y, Miller DP, Liu R, Zurek E, Lu ZL, Gong B. Reverse Turn Foldamers: An Expanded β-Turn Motif Reinforced by Double Hydrogen Bonds. Org Lett 2020; 22:1003-1007. [DOI: 10.1021/acs.orglett.9b04547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Tang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, New York 11549, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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5
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Bommer M, Coates L, Dau H, Zouni A, Dobbek H. Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO. Acta Crystallogr F Struct Biol Commun 2017; 73:525-531. [PMID: 28876232 PMCID: PMC5619745 DOI: 10.1107/s2053230x17012171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3 crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.
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Affiliation(s)
- Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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6
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Bommer M, Bondar AN, Zouni A, Dobbek H, Dau H. Crystallographic and Computational Analysis of the Barrel Part of the PsbO Protein of Photosystem II: Carboxylate–Water Clusters as Putative Proton Transfer Relays and Structural Switches. Biochemistry 2016; 55:4626-35. [DOI: 10.1021/acs.biochem.6b00441] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Martin Bommer
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Fachbereich
Physik, Theoretical Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut
für Biologie, Biophysik der Photosynthese, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dau
- Fachbereich
Physik, Biophysics and Photosynthesis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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7
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Kang YK, Yoo IK. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures. Biopolymers 2016; 105:653-64. [DOI: 10.1002/bip.22863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
- LG Research Park, LG Household & Health Care; Daejeon 34114 Republic of Korea
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8
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Bandyopadhyay A, Misra R, Gopi HN. Structural features and molecular aggregations of designed triple-stranded β-sheets in single crystals. Chem Commun (Camb) 2016; 52:4938-41. [DOI: 10.1039/c6cc00127k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Design, synthesis, single-crystal conformations and molecular aggregations of hybrid triple-stranded β-sheets, and their structural analogy with protein structures are reported.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Rajkumar Misra
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Hosahudya N. Gopi
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
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9
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Kang YK, Park HS. Propensities to form the β-turn and β-hairpin structures of d-Pro-Gly and Aib- d-Ala containing peptides: a computational study. NEW J CHEM 2016. [DOI: 10.1039/c6nj00614k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Significantly improved thermostability of a reductase CgKR1 from Candida glabrata with a key mutation at Asp 138 for enhancing bioreduction of aromatic α-keto esters. J Biotechnol 2015; 203:54-61. [DOI: 10.1016/j.jbiotec.2015.02.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/14/2015] [Accepted: 02/28/2015] [Indexed: 01/03/2023]
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11
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Kang YK, Park HS. Hairpin formation promoted by the heterochiral dinipecotic acid segment: A DFT study. Biopolymers 2015; 103:609-17. [PMID: 26015319 DOI: 10.1002/bip.22687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 01/16/2023]
Abstract
Conformational preferences for the turn and β-hairpin structures of Ala-based peptides [Ac-Ala(n)-(R)-Nip-(S)-Nip-Ala(n)-X (n = 0-2; X = NHMe or NMe2)] containing nipecotic acid (Nip) residues were carried out using the density functional M06-2X and the implicit solvation model SMD in CH2Cl2 and/or water. The turn structure of the (R)-Nip-(S)-Nip segment with a C10 H-bond between two terminal groups was found to be most preferred (populated at 98.9%) in CH2Cl2; this structure is consistent with IR and (1)H NMR results. The stabilities of the β-hairpins containing the (R)-Nip-(S)-Nip segment as a turn motif relative to the extended structures increased with peptide sequence length. The relative strengths of the H-bonds between the carbonyl oxygen and the amide hydrogen appeared to be responsible for stabilizing the turn and β-hairpin structures in CH2Cl2. In addition, the (R)-Nip-(S)-Nip segment exhibited the capability to be incorporated into one of the two β-turn motifs of gramicidin S (GS). The structure of this GS derivative (GS-Nip2 ) was generally similar to the native peptide but was less hydrophobic and it is therefore expected to exhibit lower hemolytic activity; however, further experiments are needed to evaluate its antimicrobial activity. The structure of GS-Nip2 was somewhat more flexible than GS in solvents of higher polarity. Thus, our calculated results regarding the turn and β-hairpin motifs of the (R)-Nip-(S)-Nip segment indicate that this structure might be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics as well as binding epitopes in protein-protein and protein-nucleic acid recognitions.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team, Chungbuk National University, Cheongju, Chungbuk, 362-763, Republic of Korea
| | - Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 690-708, Republic of Korea
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12
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Körling M, Geyer A. Stabilization of a Natural β-Hairpin by a Twist-Compatible β-Turn Mimetic. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Madan B, Sokalingam S, Raghunathan G, Lee SG. Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability. Proteins 2014; 82:2812-22. [PMID: 25044033 DOI: 10.1002/prot.24644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/24/2014] [Accepted: 07/03/2014] [Indexed: 11/10/2022]
Abstract
Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns. Here, we redesigned the native Type II' β-turn in GFP to Type I' β-turn, and investigated its effect on protein folding and stability. The Type I' β-turns were designed based on the statistical analysis of residues in natural Type I' β-turns. The substitution of the native "GD" sequence of i+1 and i+2 residues with Type I' preferred "(N/D)G" sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β-turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β-turns in natural β-hairpins can be further optimized by converting the sequence to Type I'.
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Affiliation(s)
- Bharat Madan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, South Korea
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14
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Madan B, Seo SY, Lee SG. Structural and sequence features of two residue turns in beta-hairpins. Proteins 2014; 82:1721-33. [PMID: 24488781 DOI: 10.1002/prot.24526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 12/16/2022]
Abstract
Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.
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Affiliation(s)
- Bharat Madan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, South Korea
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15
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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16
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Variant of the Thermomyces lanuginosus lipase with improved kinetic stability: a candidate for enzyme replacement therapy. Biophys Chem 2013; 172:43-52. [PMID: 23357413 DOI: 10.1016/j.bpc.2012.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/08/2012] [Accepted: 12/08/2012] [Indexed: 11/21/2022]
Abstract
Lipases with high kinetic stability and enzymatic efficiency in the human gastro-intestinal tract may help against exocrine pancreatic insufficiency. Here we mimic gastric conditions to study how bile salts and pH affect the stability and activity of Thermomyces lanuginosus lipase (TlL) and its stabler variant StL using spectroscopy, calorimetry and gel electrophoresis. Both enzymes resist trypsin digestion with and without bile salts. Bile salts activate native TlL and StL equally well, bind weakly to denatured TlL and StL at lower pH and precipitate native TlL and StL at pH 4. StL refolds more efficiently than TlL from gastric pH in bile salts, regaining activity when refolding from pH as low as 1.8 and above while TlL cannot go below pH 2.6. StL also unfolds 10-40 fold more slowly in the denaturant guanidinium chloride and the anionic surfactant SDS. We ascribe StL's superior performance to general alterations in its electrostatic potential which makes it more acid-resistant. These superior properties make StL a good candidate for pancreatic enzyme replacement therapy.
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17
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Kang YK, Byun BJ. Computationally designed β-turn foldamers of γ-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid. Biopolymers 2012; 97:1018-25. [DOI: 10.1002/bip.22119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Saha I, Shamala N. Investigating diproline segments in proteins: occurrences, conformation and classification. Biopolymers 2011; 97:54-64. [PMID: 21898361 DOI: 10.1002/bip.21703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/18/2011] [Accepted: 07/18/2011] [Indexed: 11/06/2022]
Abstract
The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60 °± 30° for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (( L) Pro-( L) Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II) -P(II) and P(II) -α are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the Xaa-Pro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies.
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Affiliation(s)
- Indranil Saha
- Department of Physics, Indian Institute of Science, Bangalore, India.
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19
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Gokhale A, Weldeghiorghis TK, Taneja V, Satyanarayanajois SD. Conformationally constrained peptides from CD2 to modulate protein-protein interactions between CD2 and CD58. J Med Chem 2011; 54:5307-19. [PMID: 21755948 DOI: 10.1021/jm200004e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cell adhesion molecule CD2 and its ligand CD58 provide good examples of protein-protein interactions in cells that participate in the immune response. To modulate the cell adhesion interaction, peptides were designed from the discontinuous epitopes of the β-strand region of CD2 protein. The two strands were linked by a peptide bond. β-Strands in the peptides were nucleated by inserting a β-sheet-inducing (D)-Pro-Pro sequence or a dibenzofuran (DBF) turn mimetic with key amino acid sequences from CD2 protein that binds to CD58. The solution structures of the peptides (5-10) were studied by NMR and molecular dynamics simulations. The ability of these peptides to inhibit cell adhesion interaction was studied by E-rosetting and lymphocyte epithelial assays. Peptides 6 and 7 inhibit the cell adhesion activity with an IC(50) of 7 and 11 nM, respectively, in lymphocyte epithelial adhesion assay. NMR and molecular modeling results indicated that peptides 6 and 7 exhibited β-hairpin structure in solution.
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Affiliation(s)
- Ameya Gokhale
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana 71201, United States
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20
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Jakob RP, Zierer BK, Weininger U, Hofmann SD, Lorenz SH, Balbach J, Dobbek H, Schmid FX. Elimination of a cis-Proline-Containing Loop and Turn Optimization Stabilizes a Protein and Accelerates Its Folding. J Mol Biol 2010; 399:331-46. [DOI: 10.1016/j.jmb.2010.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 03/31/2010] [Accepted: 04/02/2010] [Indexed: 10/19/2022]
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21
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Fu H, Grimsley GR, Razvi A, Scholtz JM, Pace CN. Increasing protein stability by improving beta-turns. Proteins 2010; 77:491-8. [PMID: 19626709 DOI: 10.1002/prot.22509] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. We studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and measuring the stability. These two residues are statistically preferred in some beta-turn positions. We studied: Cold shock protein B (CspB), Histidine-containing phosphocarrier protein, Ubiquitin, Ribonucleases Sa2, Sa3, T1, and HI, Tryptophan synthetase alpha-subunit, and Maltose binding protein. Of the 15 single proline mutations, 11 increased stability (Average = 0.8 +/- 0.3; Range = 0.3-1.5 kcal/mol), and the stabilizing effect of double proline mutants was additive. On the basis of this and our previous work, we conclude that proteins can generally be stabilized by replacing nonproline residues with proline residues at the i + 1 position of Type I and II beta-turns and at the i position in Type II beta-turns. Other turn positions can sometimes be used if the phi angle is near -60 degrees for the residue replaced. It is important that the side chain of the residue replaced is less than 50% buried. Identical substitutions in beta-turns in related proteins give similar results. Proline substitutions increase stability mainly by decreasing the entropy of the denatured state. In contrast, the large, diverse group of proteins considered here had almost no residues in beta-turns that could be replaced by Gly to increase protein stability. Improving beta-turns by substituting Pro residues is a generally useful way of increasing protein stability.
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Affiliation(s)
- Hailong Fu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
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22
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Rea AM, Simpson ER, Meldrum JK, Williams HEL, Searle MS. Aromatic residues engineered into the beta-turn nucleation site of ubiquitin lead to a complex folding landscape, non-native side-chain interactions, and kinetic traps. Biochemistry 2009; 47:12910-22. [PMID: 18991391 DOI: 10.1021/bi801330r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fast folding of small proteins is likely to be the product of evolutionary pressures that balance the search for native-like contacts in the transition state with the minimum number of stable non-native interactions that could lead to partially folded states prone to aggregation and amyloid formation. We have investigated the effects of non-native interactions on the folding landscape of yeast ubiquitin by introducing aromatic substitutions into the beta-turn region of the N-terminal beta-hairpin, using both the native G-bulged type I turn sequence (TXTGK) as well as an engineered 2:2 XNGK type I' turn sequence. The N-terminal beta-hairpin is a recognized folding nucleation site in ubiquitin. The folding kinetics for wt-Ub (TLTGK) and the type I' turn mutant (TNGK) reveal only a weakly populated intermediate, however, substitution with X = Phe or Trp in either context results in a high propensity to form a stable compact intermediate where the initial U-->I collapse is visible as a distinct kinetic phase. The introduction of Trp into either of the two host turn sequences results in either complex multiphase kinetics with the possibility of parallel folding pathways, or formation of a highly compact I-state stabilized by non-native interactions that must unfold before refolding. Sequence substitutions with aromatic residues within a localized beta-turn capable of forming non-native hydrophobic contacts in both the native state and partially folded states has the undesirable consequence that folding is frustrated by the formation of stable compact intermediates that evolutionary pressures at the sequence level may have largely eliminated.
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Affiliation(s)
- Anita M Rea
- Centre for Biomolecular Sciences,School of Chemistry, University Park, Nottingham NG7 2RD, UK
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23
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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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24
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Marcelino AMC, Gierasch LM. Roles of beta-turns in protein folding: from peptide models to protein engineering. Biopolymers 2008; 89:380-91. [PMID: 18275088 PMCID: PMC2904567 DOI: 10.1002/bip.20960] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.
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25
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Vázquez-Figueroa E, Chaparro-Riggers J, Bommarius AS. Development of a Thermostable Glucose Dehydrogenase by a Structure-Guided Consensus Concept. Chembiochem 2007; 8:2295-301. [DOI: 10.1002/cbic.200700500] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Affiliation(s)
| | - Brian R. Linton
- Department of Chemistry, Bowdoin College, Brunswick, Maine 04011
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Hadley EB, Witek AM, Freire F, Peoples AJ, Gellman SH. Thermodynamic Analysis of β-Sheet Secondary Structure by Backbone Thioester Exchange. Angew Chem Int Ed Engl 2007; 46:7056-9. [PMID: 17691093 DOI: 10.1002/anie.200702449] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Erik B Hadley
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53726, USA
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28
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Hadley E, Witek A, Freire F, Peoples A, Gellman S. Thermodynamic Analysis of β-Sheet Secondary Structure by Backbone Thioester Exchange. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Woods RJ, Brower JO, Castellanos E, Hashemzadeh M, Khakshoor O, Russu WA, Nowick JS. Cyclic modular beta-sheets. J Am Chem Soc 2007; 129:2548-58. [PMID: 17295482 PMCID: PMC2597679 DOI: 10.1021/ja0667965] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of peptide beta-hairpins is problematic, because folding depends on the amino acid sequence and changes to the sequence can significantly decrease folding. Robust beta-hairpins that can tolerate such changes are attractive tools for studying interactions involving protein beta-sheets and developing inhibitors of these interactions. This paper introduces a new class of peptide models of protein beta-sheets that addresses the problem of separating folding from the sequence. These model beta-sheets are macrocyclic peptides that fold in water to present a pentapeptide beta-strand along one edge; the other edge contains the tripeptide beta-strand mimic Hao [JACS 2000, 122, 7654] and two additional amino acids. The pentapeptide and Hao-containing peptide strands are connected by two delta-linked ornithine (deltaOrn) turns [JACS 2003, 125, 876]. Each deltaOrn turn contains a free alpha-amino group that permits the linking of individual modules to form divalent beta-sheets. These "cyclic modular beta-sheets" are synthesized by standard solid-phase peptide synthesis of a linear precursor followed by solution-phase cyclization. Eight cyclic modular beta-sheets 1a-1h containing sequences based on beta-amyloid and macrophage inflammatory protein 2 were synthesized and characterized by 1H NMR. Linked cyclic modular beta-sheet 2, which contains two modules of 1b, was also synthesized and characterized. 1H NMR studies show downfield alpha-proton chemical shifts, deltaOrn delta-proton magnetic anisotropy, and NOE cross-peaks that establish all compounds but 1c and 1g to be moderately or well folded into a conformation that resembles a beta-sheet. Pulsed-field gradient NMR diffusion experiments show little or no self-association at low (=2 mM) concentrations. Changes to the residues in the Hao-containing strands of 1c and 1g improve folding and show that folding of the structures can be enhanced without altering the sequence of the pentapeptide strand. Well-folded cyclic modular beta-sheets 1a, 1b, and 1f each have a phenylalanine directly across from Hao, suggesting that cyclic modular beta-sheets containing aromatic residues across from Hao are better folded.
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Affiliation(s)
- R. Jeremy Woods
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Justin O. Brower
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Elena Castellanos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Mehrnoosh Hashemzadeh
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Wade A. Russu
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
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30
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Hsu HJ, Chang HJ, Peng HP, Huang SS, Lin MY, Yang AS. Assessing computational amino acid beta-turn propensities with a phage-displayed combinatorial library and directed evolution. Structure 2007; 14:1499-510. [PMID: 17027499 DOI: 10.1016/j.str.2006.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 07/28/2006] [Accepted: 08/01/2006] [Indexed: 10/24/2022]
Abstract
Structure propensities of amino acids are important determinants in guiding proteins' local and global structure formation. We constructed a phage display library--a hexa-HIS tag upstream of a CXXC (X stands for any of the 20 natural amino acids) motif appending N-terminal to the minor capsid protein pIII of M13KE filamentous phage--and developed a novel directed-evolution procedure to select for amino acid sequences forming increasingly stable beta-turns in the disulfide-bridged CXXC motif. The sequences that emerged from the directed-evolution cycles were in good agreement with type II beta-turn propensities derived from surveys of known protein structures, in particular, Pro-Gly forming a type II beta-turn. The agreement strongly supported the notion that beta-turn formation plays an active role in initiating local structure folding in proteins.
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Affiliation(s)
- Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115, Taiwan
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31
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Hughes RM, Waters ML. Model systems for β-hairpins and β-sheets. Curr Opin Struct Biol 2006; 16:514-24. [PMID: 16837192 DOI: 10.1016/j.sbi.2006.06.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 05/16/2006] [Accepted: 06/27/2006] [Indexed: 11/18/2022]
Abstract
beta-Sheets and alpha-helices are the two principal secondary structures in proteins. However, our understanding of beta-sheet structure lags behind that of alpha-helices, largely because, until recently, there was no model system to study the beta-sheet secondary structure in isolation. With the development of well-folded beta-hairpins, this is changing rapidly. Recent advances include: increased understanding of the relative contributions of turn, strand and sidechain interactions to beta-hairpin and beta-sheet stability, with the role of aromatic residues as a common subtheme; experimental and theoretical kinetic and thermodynamic studies of beta-hairpin and beta-sheet folding; de novo protein design, including all-beta structures, mixed alpha/beta motifs and switchable systems; and the creation of functional beta-hairpins.
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Affiliation(s)
- Robert M Hughes
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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32
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Crespo MD, Simpson ER, Searle MS. Population of On-pathway Intermediates in the Folding of Ubiquitin. J Mol Biol 2006; 360:1053-66. [PMID: 16815444 DOI: 10.1016/j.jmb.2006.05.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 05/24/2006] [Accepted: 05/25/2006] [Indexed: 11/15/2022]
Abstract
The role that intermediate states play in protein folding is the subject of intense investigation and in the case of ubiquitin has been controversial. We present fluorescence-detected kinetic data derived from single and double mixing stopped-flow experiments to show that the F45W mutant of ubiquitin (WT*), a well-studied single-domain protein and most recently regarded as a simple two-state system, folds via on-pathway intermediates. To account for the discrepancy we observe between equilibrium and kinetic stabilities and m-values, we show that the polypeptide chain undergoes rapid collapse to an intermediate whose presence we infer from a fast lag phase in interrupted refolding experiments. Double-jump kinetic experiments identify two direct folding phases that are not associated with slow isomerisation reactions in the unfolded state. These two phases are explained by kinetic partitioning which allows molecules to reach the native state from the collapsed state via two possible competing routes, which we further examine using two destabilised ubiquitin mutants. Interrupted refolding experiments allow us to observe the formation and decay of an intermediate along one of these pathways. A plausible model for the folding pathway of ubiquitin is presented that demonstrates that obligatory intermediates and/or chain collapse are important events in restricting the conformational search for the native state of ubiquitin.
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Affiliation(s)
- Maria D Crespo
- Centre for Biomolecular Sciences, School of Chemistry, University Park, Nottingham NG7 2RD, UK
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Rai R, Raghothama S, Balaram P. Design of a Peptide Hairpin Containing a Central Three-Residue Loop. J Am Chem Soc 2006; 128:2675-81. [PMID: 16492054 DOI: 10.1021/ja056861v] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The construction of a designed beta-hairpin structure, containing a central three-residue loop has been successfully achieved in the synthetic nonapeptide Boc-Leu-Phe-Val-(D)Pro-(L)Pro-(D)Ala-Leu-Phe-Val-OMe (2). The design is based on expanding the two-residue loop established in the peptide beta-hairpin Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1). Characterization of the registered beta-hairpins in peptides 1 and 2 is based on the observation of key nuclear Overhauser effects (NOEs) in CDCl(3) and CD(3)OH. Solvent titration and temperature dependence of NH chemical shifts establish the identity of NH groups involved in interstrand hydrogen bonding. In peptide 2, the antiparallel registry is maintained, with the formation of a (D)Pro-(L)Pro-(D)Ala loop, stabilized by a 5-->1 hydrogen bond between Val3 CO and Leu7 NH groups (C(13), alpha-turn) and a 3-->1 hydrogen bond between (D)Pro4 CO and (d)Ala6 NH groups (C(7), gamma-turn). NMR derived structures suggest that in peptide 2, (d)Ala(6) adopts an alpha(L) conformation. In peptide 1, the (D)Pro-(L)Pro segment adopts a type II' beta-turn. Replacement of (D)Ala (6) in peptide 2 by (L)Ala in peptide 3 yields a beta-hairpin conformation, with a central (D)Pro-(L)Pro two-residue loop. Strand slippage at the C-terminus results in altered registry of the antiparallel strands.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit and NMR Research Center, Indian Institute of Science, Bangalore
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