1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Silk MR, Price JR, Mohanty B, Leiros HKS, Lund BA, Thompson PE, Chalmers DK. Side-Chain Interactions in d/l Peptide Nanotubes: Studies by Crystallography, NMR Spectroscopy and Molecular Dynamics. Chemistry 2021; 27:14489-14500. [PMID: 34415083 DOI: 10.1002/chem.202102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/07/2022]
Abstract
Our understanding of the factors affecting the stability of cyclic d/l peptide (CP) nanotubes remains underdeveloped. In this work, we investigate the impact of side chain alignment, hydrophobicity and charge on CP nanotube stability through X-ray crystallography, NMR spectroscopy and molecular dynamics (MD) simulations. We characterise the distinct CP-CP alignments that can form and identify stable and unstable dimers by MD simulation. We measure H-bond half-lives of synthesised CPs by 1 H-D exchange experiments and find good correlation with predicted CP-CP stabilities. We find that hydrophobic amino acids improve CP dimer stability but experimentally reduce solubility. Charged amino acids either increase or decrease CP dimer stability depending on the relative orientation and composition of charged groups. X-ray crystal structures are solved for two CPs, revealing non-tubular folded conformations. Ultimately, this work will assist the educated design of stable tubular structures for potential applications in biomedicine.
Collapse
Affiliation(s)
- Mitchell R Silk
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Jason R Price
- Australian Synchrotron, The Australian Nuclear Science and Technology Organisation (ANSTO), 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Bjarte A Lund
- Department of Chemistry, UiT - The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| |
Collapse
|
5
|
Chiu HS, Horng JC. Modulating the Stability of Collagen Triple Helices by Terminal Charged Residues. J Phys Chem B 2021; 125:7351-7358. [PMID: 34213353 DOI: 10.1021/acs.jpcb.1c01631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cationic or anionic residues are frequently located at the termini of proteins because their charged side chain can form electrostatic interactions with a terminal carboxylate or ammonium group to stabilize the structure under physiological conditions. Here, we used collagen-mimetic peptides (CMPs) to examine how the terminal charge-charge interactions affect the collagen triple helix stability. We designed a series of CMPs with either a Lys or Glu incorporated into the terminus and measured their pH-dependent stability. The results showed that the terminal electrostatic attractions stabilized the triple helix, while the terminal electrostatic repulsions destabilized the trimer. The data also revealed that the repulsions imposed a greater effect than did the attractions on the triple helix. An amino acid with a shorter side chain, such as aspartate and ornithine, was also installed to investigate the length effect on electrostatic interactions, which was found to be insignificant. Meanwhile, simultaneously incorporating cationic and anionic residues into the termini showed slight additive stabilization effects but pronounced additive destabilization consequences. We have demonstrated that the collagen triple helix stability can be modulated by introducing a cationic or anionic residue into the terminus of a peptide, giving useful information for the design of collagen-associated materials.
Collapse
Affiliation(s)
- He-Sheng Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Swapping the Positions in a Cross-Strand Lateral Ion-Pairing Interaction between Ammonium- and Carboxylate-Containing Residues in a β-Hairpin. Molecules 2021; 26:molecules26051346. [PMID: 33802596 PMCID: PMC7961788 DOI: 10.3390/molecules26051346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/20/2022] Open
Abstract
Cross-strand lateral ion-pairing interactions are important for antiparallel β-sheet stability. Statistical studies suggested that swapping the position of cross-strand lateral residues should not significantly affect the interaction. Herein, we swapped the position of ammonium- and carboxylate-containing residues with different side-chain lengths in a cross-strand lateral ion-pairing interaction in a β-hairpin. The peptides were analyzed by 2D-NMR. The fraction folded population and folding free energy were derived from the chemical shift data. The ion-pairing interaction energy was derived using double mutant cycle analysis. The general trends for the fraction folded population and interaction energetics remained similar upon swapping the position of the interacting charged residues. The most stabilizing cross-strand interactions were between short residues, similar to the unswapped study. However, the fraction folded populations for most of the swapped peptides were higher compared to the corresponding unswapped peptides. Furthermore, subtle differences in the ion-pairing interaction energy upon swapping were observed, most likely due to the “unleveled” relative positioning of the interacting residues created by the inherent right-handed twist of the structure. These results should be useful for developing functional peptides that rely on lateral ion-pairing interactions across antiparallel β-strands.
Collapse
|
8
|
Bureau HR, Quirk S, Hernandez R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv 2020; 10:6520-6535. [PMID: 35495997 PMCID: PMC9049704 DOI: 10.1039/d0ra00920b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 11/21/2022] Open
Abstract
The single-point mutations of tprzip1 are indicated at left, and their relative energetics are compared at right.
Collapse
|
9
|
Wu PY, Chen CY, Li JH, Lin JK, Chen TH, Huang SJ, Huang SL, Cheng RP. Effects of Arginine Deimination and Citrulline Side-Chain Length on Peptide Secondary Structure Formation. Chembiochem 2019; 20:2118-2124. [PMID: 31071235 DOI: 10.1002/cbic.201900231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Indexed: 01/07/2023]
Abstract
Post-translational modifications expand the chemical functionality of peptides and proteins beyond that originating from the encoded amino acids, but studies on the structural effects of these modifications have been limited. Arginine undergoes deimination to give citrulline (Cit), converting the positively charged guanidinium moiety into a neutral urea group. Herein, we report the effect of Arg deimination on secondary structure formation. To understand the reason for the number of methylene units in Cit, the effect of Cit side-chain length on secondary structure formation was also studied. Ala-based peptides and β-hairpin peptides were used to study α-helix and β-sheet formation, respectively. Peptides containing Cit analogues were prepared by an orthogonal protecting group strategy coupled with solid-phase carbamylation. The CD data for the Ala-based peptides were analyzed by using modified Lifson-Roig theory, showing that the helix propensity of Arg decreased upon deimination and that either shortening or lengthening Cit also decreased the helix propensity. The β-hairpin peptides were analyzed by NMR methods, showing minimal change in strand formation energetics upon Arg deimination. Altering the Cit side-chain length did not affect strand formation energetics either. These results should be useful for the preparation of urea-bearing systems and the design of peptides incorporating urea-bearing residues with varying side-chain length.
Collapse
Affiliation(s)
- Po-Yi Wu
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Chin-Yi Chen
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Jhe-Hao Li
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Jin-Kai Lin
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Ting-Hsuan Chen
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Shing-Jong Huang
- Instrument Center, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Shou-Ling Huang
- Instrument Center, National (Taiwan) University, Taipei, 10617, Taiwan
| | - Richard P Cheng
- Department of Chemistry, National (Taiwan) University, Taipei, 10617, Taiwan
| |
Collapse
|
10
|
Bureau HR, Hershkovits E, Quirk S, Hernandez R. Determining the Energetics of Small β-Sheet Peptides using Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2016; 12:2028-37. [PMID: 26930270 DOI: 10.1021/acs.jctc.5b01110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated using an adaptive variant of the original steered molecular dynamics method called adaptive steered molecular dynamics (ASMD). The ASMD method makes it possible to perform energetic calculations on increasingly complex biological systems. Although the two peptides are similar in length and have similar secondary structures, their unfolding energetics are quite different. The hydrogen bonding profile and specific residue pair interaction energies provide insight into the differing stabilities of these peptides and reveal which of the pairs provides the most significant stabilization.
Collapse
Affiliation(s)
- Hailey R Bureau
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Eli Hershkovits
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation , Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
11
|
Zhang T, Fu DY, Wu Y, Wang Y, Wu L. A fluorescence-enhanced inorganic probe to detect the peptide and capsid protein of human papillomavirus in vitro. RSC Adv 2016. [DOI: 10.1039/c6ra00105j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A europium-substituted polyoxometalate (EuW10) could be used as a fluorescence-enhanced probe to detect the recombinant HPV L1 protein in vitro.
Collapse
Affiliation(s)
- Teng Zhang
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- China
| | - Ding-Yi Fu
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- China
| | - Yizhan Wang
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- China
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|