1
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Shao C, Wang Y, Li G, Guan H, Zhu Y, Zhang L, Dong N, Shan A. Novel design of simplified β-hairpin antimicrobial peptide as a potential food preservative based on Trp-pocket backbone. Food Chem 2024; 448:139128. [PMID: 38574714 DOI: 10.1016/j.foodchem.2024.139128] [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: 12/24/2023] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Food contamination from microbial deterioration requires the development of potent antimicrobial peptides (AMPs). The deployment of approved AMPs as dietary preservatives is limited due to barriers such as instability, toxicity, and high synthetic costs. This exploration utilizes the primary structural elements of the Trp-pocket backbone to engineer a series of β-hairpin AMPs (XWRWRPGXKXXR-NH2, X representing I, V, F, and/or L). Peptides WpLF, with Phe as X and Leu arranged at the 11th position, demonstrated exceptional selectivity index (SI = 123.08) and sterilization effects both in vitro and in vivo. WpLF consistently exhibited stable bacteriostasis, regardless of physiological salts, serum, and extreme pH. Mechanistic analysis indicated that the peptide penetrates microbial cell membranes, inducing membrane disruption, thereby impeding drug resistance evolution. Conclusively, AMPs engineered by the Trp-pocket skeleton hold substantial potential as innovative biological preservatives in food preservation, providing valuable insights for sustainable and safe peptide-based food preservatives.
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Affiliation(s)
- Changxuan Shao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Yuanmengxue Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Guoyu Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Hongrui Guan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Yongjie Zhu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Licong Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Na Dong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Anshan Shan
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
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2
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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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3
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Li NZ, Yu CH, Wu JY, Huang SJ, Huang SL, Cheng RP. Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a β-Hairpin. Molecules 2023; 28:molecules28072888. [PMID: 37049652 PMCID: PMC10096425 DOI: 10.3390/molecules28072888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Cross-strand interactions are important for the stability of β-sheet structures. Accordingly, cross-strand diagonal interactions between glutamate and arginine analogs with varying side-chain lengths were studied in a series of β-hairpin peptides. The peptides were analyzed by homonuclear two-dimensional nuclear magnetic resonance methods. The fraction folded population and folding free energy of the peptides were derived from the chemical shift data. The fraction folded population trends could be rationalized using the strand propensity of the constituting residues, which was not the case for the peptides with lysine analogs, highlighting the difference between the arginine analogs and lysine analogs. Double-mutant cycle analysis was used to derive the diagonal ion-pairing interaction energetics. The most stabilizing diagonal cross-strand interaction was between the shortest residues (i.e., Asp2-Agp9), most likely due to the least side-chain conformational penalty for ion-pair formation. The diagonal interaction energetics in this study involving the arginine analogs appears to be consistent with and extend beyond our understanding of diagonal ion-pairing interactions involving lysine analogs. The results should be useful for designing β-strand-containing molecules to affect biological processes such as amyloid formation and protein-protein interactions.
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Affiliation(s)
- Nian-Zhi Li
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Hsu Yu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Jhuan-Yu Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei 10617, Taiwan
| | - Shou-Ling Huang
- Instrumentation Center, National Taiwan University, Taipei 10617, Taiwan
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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4
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The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin. Molecules 2022; 27:molecules27134172. [PMID: 35807421 PMCID: PMC9268152 DOI: 10.3390/molecules27134172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/02/2023] Open
Abstract
The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.
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5
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Fiore KE, Patist MJ, Giannakoulias S, Huang CH, Verma H, Khatri B, Cheng RP, Chatterjee J, Petersson EJ. Structural impact of thioamide incorporation into a β-hairpin. RSC Chem Biol 2022; 3:582-591. [PMID: 35656485 PMCID: PMC9092430 DOI: 10.1039/d1cb00229e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Martijn J Patist
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Cheng-Hsin Huang
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
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6
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Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. J Am Chem Soc 2022; 144:2535-2545. [PMID: 35108000 PMCID: PMC8923077 DOI: 10.1021/jacs.1c09902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.
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Affiliation(s)
- Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Rodney Park
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
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7
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Stanojlovic V, Müller A, Moazzam A, Hinterholzer A, Ożga K, Berlicki Ł, Schubert M, Cabrele C. A Conformationally Stable Acyclic β-Hairpin Scaffold Tolerating the Incorporation of Poorly β-Sheet-Prone Amino Acids. Chembiochem 2022; 23:e202100604. [PMID: 34856053 PMCID: PMC9299858 DOI: 10.1002/cbic.202100604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Indexed: 11/09/2022]
Abstract
The β-hairpin is a structural element of native proteins, but it is also a useful artificial scaffold for finding lead compounds to convert into peptidomimetics or non-peptide structures for drug discovery. Since linear peptides are synthetically more easily accessible than cyclic ones, but are structurally less well-defined, we propose XWXWXpPXK(/R)X(R) as an acyclic but still rigid β-hairpin scaffold that is robust enough to accommodate different types of side chains, regardless of the secondary-structure propensity of the X residues. The high conformational stability of the scaffold results from tight contacts between cross-strand cationic and aromatic side chains, combined with the strong tendency of the d-Pro-l-Pro dipeptide to induce a type II' β-turn. To demonstrate the robustness of the scaffold, we elucidated the NMR structures and performed molecular dynamics (MD) simulations of a series of peptides displaying mainly non-β-branched, poorly β-sheet-prone residues at the X positions. Both the NMR and MD data confirm that our acyclic β-hairpin scaffold is highly versatile as regards the amino-acid composition of the β-sheet face opposite to the cationic-aromatic one.
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Affiliation(s)
- Vesna Stanojlovic
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Anna Müller
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Ali Moazzam
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
- School of ChemistryCollege of ScienceUniversity of TehranP.O. Box 14155–6619TehranIran
| | - Arthur Hinterholzer
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Katarzyna Ożga
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Łukasz Berlicki
- Department of Bioorganic ChemistryFaculty of ChemistryWrocław University of Science and TechnologyWybrzeże Wyspiańskiego 2750-370WrocławPoland
| | - Mario Schubert
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
| | - Chiara Cabrele
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 345020SalzburgAustria
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8
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Draper SRE, Jones ZB, Earl SO, Dalley NA, Ashton DS, Carter AJ, Conover BM, Price JL. PEGylation Increases the Strength of a Nearby NH-π Hydrogen Bond in the WW Domain. Biochemistry 2021; 60:2064-2070. [PMID: 34137579 DOI: 10.1021/acs.biochem.1c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we show that an NH-π interaction between a highly conserved Asn and a nearby Trp stabilizes the WW domain of the human protein Pin1. The strength of this NH-π interaction depends on the structure of the arene, with NH-π interactions involving Trp or naphthylalanine being substantially more stabilizing than those involving Tyr or Phe. Calculations suggest arene size and polarizability are key structural determinants of NH-π interaction strength. Methylation or PEGylation of the Asn side-chain amide nitrogen each strengthens the associated NH-π interaction, though likely for different reasons. We hypothesize that methylation introduces steric clashes that destabilize conformations in which the NH-π interaction is not possible, whereas PEGylation strengthens the NH-π interaction via localized desolvation of the protein surface.
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Affiliation(s)
| | | | - Seth O Earl
- Brigham Young University, Provo, Utah 84602, United States
| | | | | | | | | | - Joshua L Price
- Brigham Young University, Provo, Utah 84602, United States
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9
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Li Q, Li J, Yu W, Wang Z, Li J, Feng X, Wang J, Shan A. De novo design of a pH-triggered self-assembled β-hairpin nanopeptide with the dual biological functions for antibacterial and entrapment. J Nanobiotechnology 2021; 19:183. [PMID: 34127004 PMCID: PMC8201815 DOI: 10.1186/s12951-021-00927-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/04/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Acid-tolerant enteric pathogens can evade small intestinal acid barriers, colonize and infect the intestinal tract. However, broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function. RESULTS A pH-triggered dual biological functional self-assembled peptide (SAP) was designed according to the features of amino-acid building blocks and the diagonal cation-π interaction principle. The results of characterization experiments showed that changes in pH conditions could trigger microstructural transformation of the nanopeptide from nanospheres to nanofibers. The subsequent antibacterial and toxicity experiments determined that SAP had great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus above 15.6 μg/mL under acidic conditions by disrupting bacterial membrane integrity, excellent biocompatibility in vitro even at 250 μg/mL and high tolerance in physical environment. Moreover, at peptide concentrations greater than 62.5 μg/mL, SAP showed the entrapment property, which played an important role in phagocytic clearance in infection forces. Meanwhile, the in vivo results revealed that SAP possessed excellent therapeutic effect and good biosafety. CONCLUSIONS Our study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide, and established an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infections.
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Affiliation(s)
- Qiuke Li
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jinze Li
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Weikang Yu
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Zhihua Wang
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jiawei Li
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Xingjun Feng
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jiajun Wang
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China.
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, The Institute of Animal Nutrition, Northeast Agricultural University, Harbin, People's Republic of China.
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10
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Chang JY, Li NZ, Wang WM, Liu CT, Yu CH, Chen YC, Lu D, Lin PH, Huang CH, Kono O, Yang TY, Sun YT, Huang PY, Pan YJ, Chen TH, Liu MC, Huang SL, Huang SJ, Cheng RP. Longer charged amino acids favor β-strand formation in hairpin peptides. J Pept Sci 2021; 27:e3333. [PMID: 34114290 DOI: 10.1002/psc.3333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/11/2022]
Abstract
Interactions between charged amino acids significantly influence the structure and function of proteins. The encoded charged amino acids Asp, Glu, Arg, and Lys have different number of hydrophobic methylenes linking the backbone to the charged functionality. It remains to be fully understood how does this difference in the number of methylenes affect protein structure stability. Protein secondary structures are the fundamental three-dimensional building blocks of protein structures. β-Sheet structures are particularly interesting, because these structures have been associated with a number of protein misfolding diseases. Herein, we report the effect of charged amino acid side chain length at two β-strand positions individually on the stability of a β-hairpin. The charged amino acids include side chains with a carboxylate, an ammonium, or a guanidinium group. The experimental peptides, fully folded reference peptides, and fully unfolded reference peptides were synthesized by solid phase peptide synthesis and analyzed by 2D NMR methods including TOCSY, DQF-COSY, and ROESY. Sequence specific assignments were performed for all peptides. The chemical shift data were used to derive the fraction folded population and the folding free energy for the experimental peptides. Results showed that the fraction folded population increased with increasing charged amino acid side chain length. These results should be useful for developing functional peptides that adopt the β-conformation.
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Affiliation(s)
- Jing-Yuan Chang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Nian-Zhi Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Wei-Ming Wang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chih-Ting Liu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chen-Hsu Yu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yan-Chen Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Daniel Lu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Pei-Hsuan Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Cheng-Hsin Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Orika Kono
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Tzu-Yi Yang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Sun
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yen-Jin Pan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Mu-Chun Liu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Shou-Ling Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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11
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Practical considerations for generation of multi-compartment complex coacervates. Methods Enzymol 2020; 646:115-142. [PMID: 33453923 DOI: 10.1016/bs.mie.2020.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We discuss preparation of experimental models for multi-compartment membraneless organelles in which distinct compositions are maintained indefinitely for macromolecule-rich phases in contact with each other. These model systems are based on the physical chemistry phenomenon of complex coacervation. In complex coacervation, liquid-liquid phase separation occurs due to ion pairing interactions between oppositely charged polyelectrolytes. This mechanism can drive the associative phase separation of proteins and nucleic acids, the major macromolecular components of membraneless organelles. Here we provide examples, advice and practical considerations for the design, generation, and analysis of multi-compartment complex coacervates. These structures are of interest to compartmentalize the interior of artificial cells and as models for the intracellular membraneless organelles of biological cells.
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12
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Urmey AR, Zondlo NJ. Structural preferences of cysteine sulfinic acid: The sulfinate engages in multiple local interactions with the peptide backbone. Free Radic Biol Med 2020; 148:96-107. [PMID: 31883974 DOI: 10.1016/j.freeradbiomed.2019.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
Cysteine sulfinic acid (Cys-SO2-) is a non-enzymatic oxidative post-translational modification (PTM) that has been identified in hundreds of proteins. However, the effects of cysteine sulfination are in most cases poorly understood. Cys-SO2- is structurally distinctive, with long sulfur-carbon and sulfur-oxygen bonds, and with tetrahedral geometry around sulfur due to its lone pair. Cys-SO2- thus has a unique range of potential interactions with the protein backbone which could facilitate protein structural changes. Herein, the structural effects of cysteine oxidation to the sulfinic acid were investigated in model peptides and folded proteins using NMR spectroscopy, circular dichroism, bioinformatics, and computational studies. In the PDB, Cys-SO2- shows a greater preference for α-helix than Cys. In addition, Cys-SO2- is more commonly found in structures with φ > 0, including in multiple types of β-turn. Sulfinate oxygens engage in hydrogen bonds with adjacent (i or i + 1) amide hydrogens. Over half of sulfinates have at least one hydrogen bond with an adjacent amide, and several structures have hydrogen bonds with both adjacent amides. Alternately, sulfur or either oxygen can act as an electron donor for n→π* interactions with the backbone carbonyl of the same residue, as indicated by frequent S⋯CO or O⋯CO distances below the sums of their van der Waals radii in protein structures. In peptides, Cys-SO2- favored α-helical structure at the N-terminus, consistent with helix dipole effects and backbone hydrogen bonds with the sulfinate promoting α-helix. Cys-SO2- has only modestly greater polyproline II helix propensity than Cys-SH, likely due to competition from multiple side chain-backbone interactions. Cys-SO2- stabilizes the i+1 position of a β-turn relative to Cys-SH. Within proteins, the range of side chain-main chain interactions available to Cys-SO2- compared to Cys-SH provides a basis for potential changes in protein structure and function due to cysteine oxidation to the sulfinic acid.
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Affiliation(s)
- Andrew R Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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13
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Chen Q, Xu S, Lu X, Boeri MV, Pepelyayeva Y, Diaz EL, Soni SD, Allaire M, Forstner MB, Bahnson BJ, Rozovsky S. 77Se NMR Probes the Protein Environment of Selenomethionine. J Phys Chem B 2020; 124:601-616. [PMID: 31846581 DOI: 10.1021/acs.jpcb.9b07466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfur is critical for the correct structure and proper function of proteins. Yet, lacking a sensitive enough isotope, nuclear magnetic resonance (NMR) experiments are unable to deliver for sulfur in proteins the usual wealth of chemical, dynamic, and structural information. This limitation can be circumvented by substituting sulfur with selenium, which has similar physicochemical properties and minimal impact on protein structures but possesses an NMR compatible isotope (77Se). Here we exploit the sensitivity of 77Se NMR to the nucleus' chemical milieu and use selenomethionine as a probe for its proteinaceous environment. However, such selenium NMR spectra of proteins currently resist a reliable interpretation because systematic connections between variations of system variables and changes in 77Se NMR parameters are still lacking. To start narrowing this knowledge gap, we report here on a biological 77Se magnetic resonance data bank based on a systematically designed library of GB1 variants in which a single selenomethionine was introduced at different locations within the protein. We recorded the resulting isotropic 77Se chemical shifts and relaxation times for six GB1 variants by solution-state 77Se NMR. For four of the GB1 variants we were also able to determine the chemical shift anisotropy tensor of SeM by solid-state 77Se NMR. To enable interpretation of the NMR data, the structures of five of the GB1 variants were solved by X-ray crystallography to a resolution of 1.2 Å, allowing us to unambiguously determine the conformation of the selenomethionine. Finally, we combine our solution- and solid-state NMR data with the structural information to arrive at general insights regarding the execution and interpretation of 77Se NMR experiments that exploit selenomethionine to probe proteins.
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Affiliation(s)
- Qingqing Chen
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shiping Xu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Instrumentation and Service Center for Physical Sciences , Westlake University , Hangzhou , Zhejiang 310024 , China
| | - Michael V Boeri
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Yuliya Pepelyayeva
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Department of Microbiology & Molecular Genetics, College of Osteopathic Medicine , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Elizabeth L Diaz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sunil-Datta Soni
- Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Marc Allaire
- Berkeley Center for Structural Biology, Molecular Biophysics & Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Martin B Forstner
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Brian J Bahnson
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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14
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Neumann J, Schnurr A, Wegner HA. Perspective isomorphs - a new classification of molecular structures based on artistic and chemical concepts. Beilstein J Org Chem 2019; 15:2319-2326. [PMID: 31666866 PMCID: PMC6808190 DOI: 10.3762/bjoc.15.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/05/2019] [Indexed: 11/23/2022] Open
Abstract
Models are a quintessential part in research as well as for scientific communication in general. A special challenge is the visualization of the invisible, such as atoms and molecules. Visualizations are also deeply rooted in the discipline of art offering in the respect untapped potential in cross-fertilization with natural sciences. Here we show a new classification of molecular structures, so-called perspective isomorphs, applying an interdisciplinary crossing of epistemological concepts between chemistry and art. The idea is based on the notion that molecules can be classified, if they appear equivalent from one standpoint in a specific orientation. We termed such a group of such molecules perspective isomorphs. The general concept is outlined together with a nomenclature system. Furthermore, this concept has been visualized by artistic representations of molecules. The concept of perspective isomorphs and its discussions herein will extend current models and stimulate the discourse about the nature of atoms and molecules and especially their models.
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Affiliation(s)
- Jannis Neumann
- Justus-Liebig-Universität Gießen, Institut für Kunstpädagogik, Karl-Glöckner-Str. 21, 35394 Gießen, Germany
| | - Ansgar Schnurr
- Justus-Liebig-Universität Gießen, Institut für Kunstpädagogik, Karl-Glöckner-Str. 21, 35394 Gießen, Germany
| | - Hermann A Wegner
- Justus-Liebig-Universität Gießen, Institut für Organische Chemie, Heinrich-Buff-Ring 17, 35392 Gießen
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15
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Lee PC, Chu CC, Tsai YJ, Chuang YC, Lung FD. Design, synthesis, and antimicrobial activities of novel functional peptides against Gram-positive and Gram-negative bacteria. Chem Biol Drug Des 2019; 94:1537-1544. [PMID: 31059203 DOI: 10.1111/cbdd.13535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/08/2019] [Accepted: 04/18/2019] [Indexed: 12/29/2022]
Abstract
The extensive use of antibiotics in medicine results in the multidrug resistance of bacteria, making the development of new antimicrobial agents an urgent need. Antimicrobial peptides (AMPs) are considered as a new class of antibiotic with characteristics including an ability to kill target cells rapidly and a broad spectrum of activity. We have developed a potent antimicrobial peptide MAP-0403 (MIC = 5 μM), but it exhibited a high hemolytic side-effect (70.7%). To reduce its hemolytic effect and increase antimicrobial activity, three peptides derivatives of MAP-0403 (J-1, J-2, and J-3) were designed, synthesized by solid phase synthesis, purified by RP-HPLC, and characterized by MALDI-TOF MS. Structure-activity relationships of these peptides were studied by using circular dichroism and antimicrobial assays. The percentage of helical structure in J-1, J-2, and J-3 was lower than that of MAP-0403. The antimicrobial activity of J-1 was the same as that of MAP-0403 (MIC = 5 μM), J-2 exhibited the highest activity (MIC = 2.5 μM), while J-3 showed decreased activity (MIC = 10 μM). Compared to MAP-0403, J-2 showed significantly reduced hemolytic effect (3.4%), while J-1 and J-3 showed slightly decreased hemolytic effect (46.2%, 55.6%, respectively). Peptide J-2 was discovered as a novel and potent antimicrobial agents.
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Affiliation(s)
- Ping-Chien Lee
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Chia-Chun Chu
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Yi-Je Tsai
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Ya-Chu Chuang
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Feng-Di Lung
- Department of Chemistry, Tunghai University, Taichung, Taiwan
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16
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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17
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Patterns of cation binding to the aromatic amino acid R groups in Trp, Tyr, and Phe. Comput Biol Chem 2018; 72:11-15. [DOI: 10.1016/j.compbiolchem.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/20/2017] [Accepted: 12/26/2017] [Indexed: 11/24/2022]
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18
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Diana D, Di Salvo C, Celentano V, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. Conformational stabilization of a β-hairpin through a triazole–tryptophan interaction. Org Biomol Chem 2018; 16:787-795. [DOI: 10.1039/c7ob02815f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triazole and indole rings stabilize a β-hairpin conformation through an aromatic–aromatic interaction.
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Affiliation(s)
| | | | | | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini
- CNR
- Napoli
- Italy
| | | | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali
- Biologiche e Farmaceutiche
- Università della Campania “L. Vanvitelli”
- Caserta
- Italy
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19
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Smith MS, Lawrence EEK, Billings WM, Larsen KS, Bécar NA, Price JL. An Anion-π Interaction Strongly Stabilizes the β-Sheet Protein WW. ACS Chem Biol 2017; 12:2535-2537. [PMID: 28886246 DOI: 10.1021/acschembio.7b00768] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anions have long been known to engage in stabilizing interactions with electron-deficient arenes. However, the precise nature and energetic contribution of anion-π interactions to protein stability remains a subject of debate. Here, we show that placing a negatively charged Asp in close proximity to electron-rich Phe in a reverse turn within the WW domain results in a favorable interaction that increases WW conformational stability by -1.3 kcal/mol.
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Affiliation(s)
- Mason S. Smith
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Eliza E. K. Lawrence
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Wendy M. Billings
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kimberlee S. Larsen
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Natalie A. Bécar
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L. Price
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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20
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Waters ML. From supramolecular chemistry to the nucleosome: studies in biomolecular recognition. Beilstein J Org Chem 2016; 12:1863-1869. [PMID: 27829892 PMCID: PMC5082656 DOI: 10.3762/bjoc.12.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/05/2016] [Indexed: 11/23/2022] Open
Abstract
This review highlights the author’s indirect path to research at the interface of supramolecular chemistry and chemical biology.
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Affiliation(s)
- Marcey L Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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21
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Stewart AL, Lorts AR, Seal EL, Takas NJ, Fortenberry RC. The role of sodium ions in the solubility of peptides. Struct Chem 2016. [DOI: 10.1007/s11224-016-0825-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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23
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Craven TW, Cho MK, Traaseth NJ, Bonneau R, Kirshenbaum K. A Miniature Protein Stabilized by a Cation-π Interaction Network. J Am Chem Soc 2016; 138:1543-50. [PMID: 26812069 PMCID: PMC4867217 DOI: 10.1021/jacs.5b10285] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of folded miniature proteins is predicated on establishing noncovalent interactions that direct the self-assembly of discrete thermostable tertiary structures. In this work, we describe how a network of cation-π interactions present in proteins containing "WSXWS motifs" can be emulated to stabilize the core of a miniature protein. This 19-residue protein sequence recapitulates a set of interdigitated arginine and tryptophan residues that stabilize a distinctive β-strand:loop:PPII-helix topology. Validation of the compact fold determined by NMR was carried out by mutagenesis of the cation-π network and by comparison to the corresponding disulfide-bridged structure. These results support the involvement of a coordinated set of cation-π interactions that stabilize the tertiary structure.
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Affiliation(s)
- Timothy W. Craven
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
| | - Min-Kyu Cho
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Nathaniel J. Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY
- Simons Center for Data Analysis, New York, NY
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
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24
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Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. Probing the Ca(2+)-assisted π-π interaction during Ca(2+)-dependent protein folding. SOFT MATTER 2016; 12:531-541. [PMID: 26489523 DOI: 10.1039/c5sm01796c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding is governed by a balance of non-covalent interactions, of which cation-π and π-π play important roles. Theoretical calculations revealed a strong cooperativity between cation-π involving alkali and alkaline earth metal ions and π-π interactions, but however, no experimental evidence was provided in this regard. Here, we characterized a Ca(2+)-binding self-processing module (SPM), which mediates a highly-specific Ca(2+)-dependent autocatalytic processing of iron-regulated protein FrpC secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis. The SPM undergoes a Ca(2+)-induced transition from an intrinsically unstructured conformation to the compact protein fold that is ultimately stabilized by the π-π interaction between two unique tryptophan residues arranged in the T-shaped orientation. Moreover, the pair of tryptophans is located in a close vicinity of a calcium-binding site, suggesting the involvement of a Ca(2+)-assisted π-π interaction in the stabilization of the tertiary structure of the SPM. This makes the SPM an excellent model for the investigation of the Ca(2+)-assisted π-π interaction during Ca(2+)-induced protein folding.
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Affiliation(s)
- Petra Matyska Liskova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 14200 Prague, Czech Republic.
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25
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Sarmah N, Bhattacharyya PK. Behaviour of cation–pi interaction in presence of external electric field. RSC Adv 2016. [DOI: 10.1039/c6ra21334k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
External electric field effects cation–π interaction.
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Affiliation(s)
- Nabajit Sarmah
- Department of Chemistry
- Arya Vidyapeeth College
- Guwahati-781016
- India
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26
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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27
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Cherny VV, Morgan D, Musset B, Chaves G, Smith SME, DeCoursey TE. Tryptophan 207 is crucial to the unique properties of the human voltage-gated proton channel, hHV1. ACTA ACUST UNITED AC 2015; 146:343-56. [PMID: 26458876 PMCID: PMC4621752 DOI: 10.1085/jgp.201511456] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 01/19/2023]
Abstract
Part of the "signature sequence" that defines the voltage-gated proton channel (H(V1)) is a tryptophan residue adjacent to the second Arg in the S4 transmembrane helix: RxWRxxR, which is perfectly conserved in all high confidence H(V1) genes. Replacing Trp207 in human HV1 (hH(V1)) with Ala, Ser, or Phe facilitated gating, accelerating channel opening by 100-fold, and closing by 30-fold. Mutant channels opened at more negative voltages than wild-type (WT) channels, indicating that in WT channels, Trp favors a closed state. The Arrhenius activation energy, Ea, for channel opening decreased to 22 kcal/mol from 30-38 kcal/mol for WT, confirming that Trp207 establishes the major energy barrier between closed and open hH(V1). Cation-π interaction between Trp207 and Arg211 evidently latches the channel closed. Trp207 mutants lost proton selectivity at pHo >8.0. Finally, gating that depends on the transmembrane pH gradient (ΔpH-dependent gating), a universal feature of H(V1) that is essential to its biological functions, was compromised. In the WT hH(V1), ΔpH-dependent gating is shown to saturate above pHi or pHo 8, consistent with a single pH sensor with alternating access to internal and external solutions. However, saturation occurred independently of ΔpH, indicating the existence of distinct internal and external pH sensors. In Trp207 mutants, ΔpH-dependent gating saturated at lower pHo but not at lower pHi. That Trp207 mutation selectively alters pHo sensing further supports the existence of distinct internal and external pH sensors. Analogous mutations in H(V1) from the unicellular species Karlodinium veneficum and Emiliania huxleyi produced generally similar consequences. Saturation of ΔpH-dependent gating occurred at the same pHo and pHi in H(V1) of all three species, suggesting that the same or similar group(s) is involved in pH sensing. Therefore, Trp enables four characteristic properties: slow channel opening, highly temperature-dependent gating kinetics, proton selectivity, and ΔpH-dependent gating.
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Affiliation(s)
- Vladimir V Cherny
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
| | - Boris Musset
- Institute of Complex Systems 4 Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gustavo Chaves
- Institute of Complex Systems 4 Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144
| | - Thomas E DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, IL 60612
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28
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Eisert RJ, Kennedy SA, Waters ML. Investigation of the β-Sheet Interactions between dHP1 Chromodomain and Histone 3. Biochemistry 2015; 54:2314-22. [DOI: 10.1021/acs.biochem.5b00024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Robyn J. Eisert
- Department
of Chemistry,
CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sarah A. Kennedy
- Department
of Chemistry,
CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department
of Chemistry,
CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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29
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Kuo HT, Liu SL, Chiu WC, Fang CJ, Chang HC, Wang WR, Yang PA, Li JH, Huang SJ, Huang SL, Cheng RP. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin. Amino Acids 2015; 47:885-98. [PMID: 25646959 DOI: 10.1007/s00726-015-1916-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
Abstract
β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.
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Affiliation(s)
- Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
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30
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Toward understanding driving forces in membrane protein folding. Arch Biochem Biophys 2014; 564:297-313. [DOI: 10.1016/j.abb.2014.07.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
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31
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Effect of stepwise microhydration on the guanidinium···π interaction. J Mol Model 2014; 20:2209. [PMID: 24691534 DOI: 10.1007/s00894-014-2209-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
The characteristics of the interaction of microhydrated guanidinium cation with the aromatic moieties present in the aromatic amino acids side chains have been studied by means of computational methods. The most stable minima found for non-hydrated complexes correspond in all cases to structures with guanidinium oriented toward the ring and interacting by means of N-H···π hydrogen bonds. The interaction becomes stronger when going from benzene (-14 kcal mol⁻¹) to phenol (-17 kcal mol⁻¹) to indole (-21 kcal mol⁻¹). These complexes are held together mainly by electrostatics, but with important contributions from induction and dispersion. The presence of a small number of water molecules significantly affects the characteristics of the complexes. Hydrogen bonds formed by water with the cation, another water molecule, or the aromatic units become more and more similar in intensity as water molecules are included in the complex, leading to a great variety of minima with similar stability but showing very different structural patterns. The behavior is similar with the three aromatic units, the differences in stability mainly being a consequence of the different strength of the cation···π contact.
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Affiliation(s)
- Ana A Rodríguez-Sanz
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X El Sabio s/n, 27002, Lugo, Spain
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32
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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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Kuo HT, Fang CJ, Tsai HY, Yang MF, Chang HC, Liu SL, Kuo LH, Wang WR, Yang PA, Huang SJ, Huang SL, Cheng RP. Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate-containing residues and lysine analogues in a β-hairpin. Biochemistry 2013; 52:9212-22. [PMID: 24328126 DOI: 10.1021/bi400974x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
β-Sheets are one of the fundamental three-dimensional building blocks for protein structures. Oppositely charged amino acids are frequently observed directly across one another in antiparallel sheet structures, suggesting the importance of cross-strand ion pairing interactions. Despite the apparent electrostatic nature of ion pairing interactions, the charged amino acids Asp, Glu, Arg, Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. Accordingly, the effect of charged amino acid side chain length on cross-strand ion pairing interactions at lateral non-hydrogen bonded positions was investigated in a β-hairpin motif. The negatively charged residues with a carboxylate (Asp, Glu, Aad in increasing length) were incorporated at position 4, and the positively charged residues with an ammonium (Dap, Dab, Orn, Lys in increasing length) were incorporated at position 9. The fraction folded population and folding free energy were derived from the chemical shift deviation data. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Only the Asp/Glu-Dap interactions with shorter side chains and the Aad-Orn/Lys interactions with longer side chains exhibited stabilizing energetics, mostly relying on electrostatics and hydrophobics, respectively. This suggested the need for length matching of the interacting residues to stabilize the β-hairpin motif. A survey of a nonredundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Lys < Glu-Lys, also implying the need for length matching of the oppositely charged residues.
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Affiliation(s)
- Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
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34
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Kuo LH, Li JH, Kuo HT, Hung CY, Tsai HY, Chiu WC, Wu CH, Wang WR, Yang PA, Yao YC, Wong TW, Huang SJ, Huang SL, Cheng RP. Effect of charged amino acid side chain length at non-hydrogen bonded strand positions on β-hairpin stability. Biochemistry 2013; 52:7785-97. [PMID: 24156236 DOI: 10.1021/bi400911p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
β-Sheets have been implicated in various neurological disorders, and ∼20% of protein residues adopt a sheet conformation. Therefore, studies on the structural origin of sheet stability can provide fundamental knowledge with potential biomedical applications. Oppositely charged amino acids are frequently observed across one another in antiparallel β-sheets. Interestingly, the side chains of natural charged amino acids Asp, Glu, Arg, Lys have different numbers of hydrophobic methylenes linking the backbone to the hydrophilic charged functionalities. To explore the inherent effect of charged amino acid side chain length on antiparallel sheets, the stability of a designed hairpin motif containing charged amino acids with varying side chain lengths at non-hydrogen bonded positions was studied. Peptides with the guest position on the N-terminal strand and the C-terminal strand were investigated by NMR methods. The charged amino acids (Xaa) included negatively charged residues with a carboxylate group (Asp, Glu, Aad in increasing length), positively charged residues with an ammonium group (Dap, Dab, Orn, Lys in increasing length), and positively charged residues with a guanidinium group (Agp, Agb, Arg, Agh in increasing length). The fraction folded and folding free energy for each peptide were derived from the chemical shift deviation data. The stability of the peptides with the charged residues at the N-terminal guest position followed the trends: Asp > Glu > Aad, Dap < Dab < Orn ∼ Lys, and Agb < Arg < Agh < Agp. The stability of the peptides with the charged residues at the C-terminal guest position followed the trends: Asp < Glu < Aad, Dap ∼ Dab < Orn ∼ Lys, and Agb < Arg ∼ Agp < Agh. These trends were rationalized by thermodynamic sheet propensity and cross-strand interactions.
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Affiliation(s)
- Li-Hung Kuo
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
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35
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Shu I, Scian M, Stewart JM, Kier BL, Andersen NH. 13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues. JOURNAL OF BIOMOLECULAR NMR 2013; 56:313-329. [PMID: 23851979 DOI: 10.1007/s10858-013-9749-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
The present studies have shown that (13)C=O, (13)C(α) and (13)C(β) of H-bonded strand residues in β-hairpins provide additional probes for quantitating the extent of folding in β-hairpins and other β-sheet models. Large differences in the structuring shifts (CSDs) of these (13)C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three (13)C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from (13)C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the (13)C' and (13)C(β) CSDs will provide the best differentiation with 100%-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein β-sheets. Our survey of reported (13)C shifts in β-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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36
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Meyer D, Mutschler C, Robertson I, Batt A, Tatko C. Aromatic interactions with naphthylalanine in a β
-hairpin peptide. J Pept Sci 2013; 19:277-82. [DOI: 10.1002/psc.2496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Meyer
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Caleb Mutschler
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Ian Robertson
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Alexandra Batt
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
| | - Chad Tatko
- Calvin College, Chemistry and Biochemistry; Grand Rapids Michigan USA
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37
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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38
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Campo-Cacharrón A, Cabaleiro-Lago EM, Rodríguez-Otero J. Effects of microhydration on the characteristics of cation–phenol complexes. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1290-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Lengyel GA, Horne WS. Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β-Sheets by α/β-Peptides. J Am Chem Soc 2012; 134:15906-13. [DOI: 10.1021/ja306311r] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- George A. Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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40
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Zheng X, Wu C, Ponder JW, Marshall GR. Molecular dynamics of β-hairpin models of epigenetic recognition motifs. J Am Chem Soc 2012; 134:15970-8. [PMID: 22934656 DOI: 10.1021/ja306803v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The conformations and stabilities of the β-hairpin model peptides of Waters (Riemen, A. J.; Waters, M. L. Biochemistry 2009, 48, 1525; Hughes, R. M.; Benshoff, M. L.; Waters, M. L. Chemistry 2007, 13, 5753) have been experimentally characterized as a function of lysine ε-methylation. These models were developed to explore molecular recognition of known epigenetic recognition motifs. This system offered an opportunity to computationally examine the role of cation-π interactions, desolvation of the ε-methylated ammonium groups, and aromatic/aromatic interactions on the observed differences in NMR spectra. AMOEBA, a second-generation force field (Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549), was chosen as it includes both multipole electrostatics and polarizability thought to be essential to accurately characterize such interactions. Independent parametrization of ε-methylated amines was required from which aqueous solvation free energies were estimated and shown to agree with literature values. Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me)(n)-I-L-Q-NH(2), where n = 0, 1, 2, or 3, were conducted in explicit solvent. Distances between the centers of the indole rings of the two-tryptophan residues, 2 and 4, and the ε-methylated ammonium group on Lys-9 as well as the distance between the N- and C-termini were monitored to estimate the strength and orientation of the cation-π and aromatic/aromatic interactions. In agreement with the experimental data, the stability of the β-hairpin increased significantly with lysine ε-methylation. The ability of MD simulations to reproduce the observed NOEs for the four peptides was further estimated for the monopole-based force fields, AMBER, CHARMM, and OPLSAA. AMOEBA correctly predicted over 80% of the observed NOEs for all 4 peptides, while the three-monopole force fields were 40-50% predictive in only 2 cases and approximately 10% in the other 10 examples. Preliminary analysis suggests that the decreased cost of desolvation of the substituted ammonium group significantly compensated for the reduced cation-π interaction resulting from the increased separation due to steric bulk of the ε-methylated amines.
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Affiliation(s)
- Xiange Zheng
- Department of Chemistry and of Biochemistry, Washington University, St. Louis, Missouri 63105, United States
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41
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Effect of stepwise microhydration on the methylammonium···phenol and ammonium···phenol interaction. J Mol Model 2012; 19:1985-94. [DOI: 10.1007/s00894-012-1579-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
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42
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43
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Lichtenstein BR, Moorman VR, Cerda JF, Wand AJ, Dutton PL. Electrochemical and structural coupling of the naphthoquinone amino acid. Chem Commun (Camb) 2012; 48:1997-9. [PMID: 22234390 DOI: 10.1039/c2cc16968a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As a prelude to engineering artificial energy conversion proteins emulating biology, we examine the inclusion of a synthetic naphthoquinone amino acid in a characterized host-guest protein and determine the effects of its quinone and hydroquinone forms on the helix-coil distribution.
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Affiliation(s)
- Bruce R Lichtenstein
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
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44
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Cabaleiro-Lago EM, Rodríguez-Otero J, Peña-Gallego Á. Effect of microhydration on the guanidinium⋯benzene interaction. J Chem Phys 2011; 135:214301. [DOI: 10.1063/1.3663277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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45
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Barry BA. Proton coupled electron transfer and redox active tyrosines in Photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2011; 104:60-71. [PMID: 21419640 PMCID: PMC3164834 DOI: 10.1016/j.jphotobiol.2011.01.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 01/25/2011] [Accepted: 01/31/2011] [Indexed: 11/30/2022]
Abstract
In this article, progress in understanding proton coupled electron transfer (PCET) in Photosystem II is reviewed. Changes in acidity/basicity may accompany oxidation/reduction reactions in biological catalysis. Alterations in the proton transfer pathway can then be used to alter the rates of the electron transfer reactions. Studies of the bioenergetic complexes have played a central role in advancing our understanding of PCET. Because oxidation of the tyrosine results in deprotonation of the phenolic oxygen, redox active tyrosines are involved in PCET reactions in several enzymes. This review focuses on PCET involving the redox active tyrosines in Photosystem II. Photosystem II catalyzes the light-driven oxidation of water and reduction of plastoquinone. Photosystem II provides a paradigm for the study of redox active tyrosines, because this photosynthetic reaction center contains two tyrosines with different roles in catalysis. The tyrosines, YZ and YD, exhibit differences in kinetics and midpoint potentials, and these differences may be due to noncovalent interactions with the protein environment. Here, studies of YD and YZ and relevant model compounds are described.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry and The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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46
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Contributions of cation–π interactions to the collagen triple helix stability. Arch Biochem Biophys 2011; 508:46-53. [DOI: 10.1016/j.abb.2011.01.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 01/07/2011] [Accepted: 01/12/2011] [Indexed: 11/20/2022]
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47
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Santiveri CM, Jiménez MA. Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides. Biopolymers 2011; 94:779-90. [PMID: 20564027 DOI: 10.1002/bip.21436] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid 28006, Spain
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48
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Sharma B, Rao JS, Sastry GN. Effect of Solvation on Ion Binding to Imidazole and Methylimidazole. J Phys Chem A 2011; 115:1971-84. [DOI: 10.1021/jp1120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Bhaskar Sharma
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - J. Srinivasa Rao
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, AP, India
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49
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Pednekar D, Durani S. Protein homomers in point-group assembly: symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains. Proteins 2011; 78:3048-55. [PMID: 20737441 DOI: 10.1002/prot.22828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Oligomerizing to point-group symmetry, protein oligomers need to have the symmetry broken for biologically crucial functions, such as, allosteric regulation, enzyme catalysis, and so forth. In the making of symmetry, based on self assembly, and the breaking of symmetry, based on intermolecular interactions, proteins may manifest, like their other functions, specific scripts over the coding alphabet in side chains. To address the possibility, we analyzed 82 protein homodimers in their C(2)-symmetry-related side chains across noncrystallographic interfaces, to know if they may be identical or distinct in conformation, and thus conserved or broken in symmetry. We find the propensity to conformational mismatch across interfaces correlated with side-chain chemical structure, low to very low in aromatic Trp, Tyr, His, Phe, and Arg, and high to very high in aliphatic Val, Pro, Met, Glu, Ser, Lys, Gln, Asn, and Asp, related not to polarity but, interestingly, to aromaticity of the structure. The organizational plan having aromatics embedded in a hub of aliphatic-nonpolar groups and a surrounding rim of aliphatic-polar groups, called "hotspot," has been known to direct protein-protein interaction. Finding conformational-mismatch propensities of side chains congruous with their specific chemical roles in protein-protein interaction, we propose that aromatic side chains will drive protein homomers to high symmetry, while polar- and nonpolar aliphatic side chains will drive them to the functionally-necessitated breaks of symmetry. Side chains are in their roles as protein-coding alphabet illuminated in the physics, which is discussed.
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Affiliation(s)
- Deepa Pednekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Mumbai 400076, India
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50
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Asandei A, Apetrei A, Park Y, Hahm KS, Luchian T. Investigation of single-molecule kinetics mediated by weak hydrogen bonds within a biological nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:19-24. [PMID: 21128603 DOI: 10.1021/la104264f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The study of factors essential for protein-peptide interactions and protein pore-mediated peptide transport are of particular relevance in biology. Wild-type α-hemolysin was adopted as a "nanoreactor" in which perturbations of the current through a protein containing a lumen-residing, aryl-capped antimicrobial peptide were seen for the first time and studied at the single-molecule level. Energy and steric considerations hint that Met-aryl interactions between aromatic residues placed at a peptide's extremities and any of the methionines lining the α-hemolysin constriction region may be the primary cause of peptide stabilization within the lumen and may be particularly important to the peptide-α-hemolysin interaction.
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Affiliation(s)
- Alina Asandei
- Department of Physics, Laboratory of Molecular Biophysics and Medical Physics, Alexandru I. Cuza University, Blvd. Carol I, No. 11, Iasi 700506, Romania
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