1
|
Fischer JL, Elvir BR, DeLucia SA, Blodgett KN, Zeller M, Kubasik MA, Zwier TS. Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation. J Phys Chem A 2019; 123:4178-4187. [PMID: 30973730 DOI: 10.1021/acs.jpca.9b01698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Joshua L. Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brayan R. Elvir
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Sally-Ann DeLucia
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Karl N. Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthew A. Kubasik
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
2
|
Li J, Wang Y, Chen J, Liu Z, Bax A, Yao L. Observation of α-Helical Hydrogen-Bond Cooperativity in an Intact Protein. J Am Chem Soc 2016; 138:1824-7. [PMID: 26853186 PMCID: PMC5575832 DOI: 10.1021/jacs.5b13140] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The presence and extent of hydrogen-bonding (H-bonding) cooperativity in proteins remains a fundamental question, which in the past has been studied extensively, mostly by infrared and fluorescence measurements on model peptides. We demonstrate that such cooperativity can be studied in an intact protein by hydrogen/deuterium exchange NMR spectroscopy. The method is based on the fact that substitution of NH by ND in a backbone amide group slightly weakens the N-H···O═C hydrogen bond. Our results show that such substitution at position i in an α-helix impacts the (1)H and (15)N chemical shifts of the amide sites of residues i - 3 to i + 3. Quantum mechanical calculations indicate that the upfield shifts of (1)H and (15)N resonances at site i, observed upon H/D exchanges at sites i - 3, i + 1, i + 2, and i + 3, correspond to a decrease of the ith backbone amide electric dipole moment, which weakens its H-bonding and long-range electrostatic interactions with other backbone amides in the α-helix. These results provide new quantitative insights into the cooperativity of H-bonding in protein α-helices.
Collapse
Affiliation(s)
- Jingwen Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao, 266061, China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao, 266061, China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Jingfei Chen
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao, 266061, China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Zhijun Liu
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao, 266061, China
- Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| |
Collapse
|
3
|
Gord JR, Hewett DM, Hernandez-Castillo AO, Blodgett KN, Rotondaro MC, Varuolo A, Kubasik MA, Zwier TS. Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former. Phys Chem Chem Phys 2016; 18:25512-25527. [PMID: 27711552 DOI: 10.1039/c6cp04909e] [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]
Abstract
Single-conformation spectroscopy is used to probe the preference for helical structural in Aib-homopeptides.
Collapse
Affiliation(s)
- Joseph R. Gord
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | | | | | | | | | - Adalgisa Varuolo
- Department of Chemistry and Biochemistry
- Fairfield University
- Fairfield
- USA
| | - Matthew A. Kubasik
- Department of Chemistry and Biochemistry
- Fairfield University
- Fairfield
- USA
| | | |
Collapse
|
4
|
Affiliation(s)
- Juan Zhao
- Beijing
National Laboratory
for Molecular Sciences; Laboratory of Molecular Reaction Dynamics,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing
National Laboratory
for Molecular Sciences; Laboratory of Molecular Reaction Dynamics,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| |
Collapse
|
5
|
Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| |
Collapse
|