Biomolecular Nmr Assignments

Biomolecular Nmr Assignments-8
This has produced a gap in this area which these webpages aim to bridge by describing the concepts of assignment in detail with the help of many illustrations.

This has produced a gap in this area which these webpages aim to bridge by describing the concepts of assignment in detail with the help of many illustrations.

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The implementation of protein NMR assignment is described using the program CCPNmr Analysis.

This program has been developed by CCPN and actively seeks input from the NMR community.

Chemical shift assignment of GTSF1 allowed site-specific observation of amide correlations, which established the basis for NMR structure calculation of GTSF1 and the evaluation of binding to candidate RNA sequences, with goal of the identification of an in vivo RNA binding partner for GTSF1.

The work presents compelling data that indicate GTSF1 Zn finger 1 specifically binds a motif GGUUC(G/A) RNA, which in this study was found in the T-arm loop of transfer RNA.

While rigid protein structures are used in classic “lock and key” descriptions of enzymology and receptor-ligand interactions, more and more evidence suggest that the majority of molecular interactions occur on the spectrum between induced-fit binding and conformational selection binding.

This model of biomolecular interaction requires, to differing degrees, conformation plasticity and dynamics of the protein itself.The facility also has available an ultrahigh sensitivity 5mm N triple-resonance cold probe for the 600 MHz spectrometers.The resources of the facility can be accessed either on a fee-for-service or on a collaborative use basis.The work presented herein involves i) the use of NMR for investigation of structure and dynamics in two separate biological systems that demonstrate a high degree of flexibility for folded proteins and ii) the improvement of pulse sequences and methodology for better characterizing picosecond to nanosecond backbone and side-chain dynamics.The organizing principle of this work, which is best exemplified in the structural studies of the pi RNA-pathway protein Gametocyte-specific factor 1, is the unmatched capability of NMR spectroscopy to decipher molecular details within dynamic protein systems.Zn finger 2 is affected by the interaction with RNA, but the available structural and binding data indicate that the second Zn finger is a more dynamic, breathable entity, supported by cysteine chemical shift and structural differences between the two GTSF1 Zn fingers.Although it’s currently speculative, the function of GTSF1 might first require binding of RNA to the more stable Zn finger 1, which then leaves Zn finger 2 poised for binding to another molecular species.First, the molecular structure and RNA-binding properties of gametocyte-specific factor 1 (GTSF1) of the pi RNA effector pathway were investigated.A partially disordered protein with two Zn finger domains, the work presented here describes the isolation of a GTSF1 protein construct amendable to study by NMR spectroscopy.To characterize the determinants and implications of protein dynamics, there exists no more suited biophysical technique than nuclear magnetic resonance (NMR) spectroscopy.This method is capable of probing the individual atomic nuclei of proteins in a site-specific manner.

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