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Peptide Bond Geometry Studied by Solid-State NMR Spectroscopy

Gupta, Chitrak
http://rave.ohiolink.edu/etdc/view?acc_num=osu1385331897

Abstract Details

2013, Master of Science, Ohio State University, Chemistry.
Three-dimensional structure of proteins is an intrinsic property of every protein, and is directly related to its biological function. Studying protein structure is thus of immense importance to understand the mechanism by which the proteins perform such functions. In principle, the backbone structure of a protein can be completely described by a set of torsional angles. Indeed, a significant amount of structural studies of proteins have involved measuring the torsional angles defined by C'-N-Cα-C' atoms (denoted φ) and N-Cα-C'-N atoms (denoted ψ). Little has been done, however, to study the third of the triplet, the ω-torsional angle, defined by the Cα-C'-N-Cα atoms, which is usually assumed to be planar, with the atoms arranged in a trans-like conformation. However, cis-like peptide bonds are known to exist, often at or near active sites, which make them biologically significant, although there are no reliable experimental methods apart from crystallographic studies to differentiate cis-peptide bonds form their trans- counterparts. This thesis is aimed at developing a new solid-state NMR experiment to study the peptide bond geometry. The primary objective is to differentiate cis- and trans-peptide bonds in polypeptides and proteins. Chapter 2 describes the synthesis of isotopically labeled model compounds with trans- and cis-peptide bond. The former, glycylglycine, was synthesized by solid phase peptide synthesis following standard protocols, with minor modifications to increase the yield. The latter, 2,5-diketopiperazine, was synthesized using microwave-assisted synthesis, a protocol recently published. Both the compounds could be obtained in high purity and integrity, as shown by their solution 1H and 13C NMR spectra. Chapter 3 describes the design of the NMR pulse sequence which can achieve this goal. The fundamental idea is to allow correlated evolution of two different anisotropic interactions under magic-angle spinning. Such evolutions are sensitive to the relative orientation of the two interactions. In this case, 13Cα-15N dipolar coupling and 13C'-13Cα dipolar coupling have been correlated, to distinguish between the two geometries about the N-C' bond. The possibility of using 13C' chemical shift anisotropy instead of 13C'-13Cα dipolar coupling has been discussed. Preliminary simulations have shown the detection of a cis-peptide bond to be possible, although, thus far, the experiment is not sensitive enough to measure deviation from planarity of a peptide bond. Chapter 4 shows the solid-state NMR spectra obtained from these model compounds. The 1D 13C and 15N CP-MAS spectra from both the compounds confirm their purity and integrity, and provide sufficient signal-to-noise to proceed with the proposed experiment. REDOR dephasing recorded on both the compounds are in good agreement with simulation. Chapter 5 discusses the future perspectives of this work, including extending it to bigger systems, and to use 15N-1H dipolar coupling instead of 13C'-13Cα dipolar coupling to increase sensitivity and enable measurement of the ω-torsional angle with reasonable accuracy.
Christopher Jaroniec (Advisor)
Thomas Magliery (Committee Member)
86 p.
Chemistry
peptide bond geometry; cis-peptide bond; omega torsional angle; solid-state NMR spectroscopy; dipolar coupling; microwave-assisted synthesis; solid phase peptide synthesis

Recommended Citations

Citations

  • Gupta, C. (2013). Peptide Bond Geometry Studied by Solid-State NMR Spectroscopy [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385331897

    APA Style (7th edition)

  • Gupta, Chitrak. Peptide Bond Geometry Studied by Solid-State NMR Spectroscopy. 2013. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1385331897.

    MLA Style (8th edition)

  • Gupta, Chitrak. "Peptide Bond Geometry Studied by Solid-State NMR Spectroscopy." Master's thesis, Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385331897

    Chicago Manual of Style (17th edition)

osu1385331897
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This open access ETD is published by The Ohio State University and OhioLINK.