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van der Wel PCA. Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy. Front Mol Biosci 2021; 8:791090. [PMID: 34938776 PMCID: PMC8685456 DOI: 10.3389/fmolb.2021.791090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.
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Affiliation(s)
- Patrick C. A. van der Wel
- Solid-state NMR Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
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Du QS, Chen D, Xie NZ, Huang RB, Chou KC. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding. J Biomol Struct Dyn 2015; 33:1957-72. [PMID: 25375237 PMCID: PMC4536944 DOI: 10.1080/07391102.2014.984333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/02/2014] [Indexed: 11/20/2022]
Abstract
Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.
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Affiliation(s)
- Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA02478, USA
| | - Dong Chen
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
| | - Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
| | - Kuo-Chen Chou
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah21589, Saudi Arabia
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA02478, USA
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Du QS, Ma Y, Xie NZ, Huang RB. Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:837-851. [PMID: 25275828 DOI: 10.1080/1062936x.2014.959049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.
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Affiliation(s)
- Q S Du
- a State Key Laboratory of Non-food Biomass and Enzyme Technology , National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences , 98 Daling Road, Nanning , China
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