Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B-Z Transition of DNA.

Kwang-Im Oh,Seo-Ree Choi,Joon-Hwa Lee,Eun-Hee Kim,Youyeon Go,Kyoung-Seok Ryu,Ae-Ree Lee

doi:10.3390/ijms22073517

Abstract

Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in μs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZαADAR1)–DNA complex. The global search results indicated that a α-helical segment of hZαADAR1 provided the main contribution to the three-state conformational changes of a hZαADAR1—DNA complex with a slow B–Z exchange process. The two global exchange rate constants, kex and kZB, were found to be 844 and 9.8 s−1, respectively, in agreement with two regimes of residue-dependent chemical shift differences—the “dominant oscillatory regime” and “semi-oscillatory regime”. We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.

Highlights

Molecular motions play important roles in biological processes; their complexity makes the accurate identification of motions difficult
ADAR1 induced by conformational transitions on a msinduced bytheconformational transitions on a dynamic of hZα to-μsThe timescale wasmotion investigated byADAR1 modeling using site-specific CPMG
relaxation dispersion (RD) shift proparameters undergoing the three-state conformational transition: (i) Residues representing the three-state conformational exchanges were determined by error of fitting using the twostate model; (ii) the residue dependent R2 profiles were numerically computed by random files

Summary

Introduction

Molecular motions play important roles in biological processes; their complexity makes the accurate identification of motions difficult. NMR spectroscopy is a powerful tool that had been used to characterize these motions according to the chemical exchanges and kinetic processes of molecules [1,2,3]. Gill (CPMG) relaxation dispersion (RD) experiments can be used to provide information on protein folding and binding events, with protein motions reported in an ms-to-μs timescale [4,5,6,7,8]. The first step of CPMG analysis is the establishment of an appropriate model to determine the exchange process. The two-state exchange process is a simple kinetic model that has been widely used to understand molecular motions, such as enzyme catalysis, protein folding, molecular recognition, and allostery, using CPMG RD analysis [1,9,10,11,12]. Despite the fact that multi-state conformational exchanges including three-state transitions have

Methods

Results

Conclusion