Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin.

Giovanni Chillemi,Maurizio Benfatto,Cristiano Padrin,Massimiliano Anselmi,Lodovico Balducci,Elisabetta Pace,Marco Cammarata,Nico Sanna,Majed Chergui

doi:10.1063/1.5031806

Abstract

We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.

Highlights

(called Minuit XANes, MXAN)) based on multiple-scattering (MS) theory which is able to extract local structural information around absorbing atoms from experimental X-ray absorption near-edge structure (XANES) data.3 The MXAN method has been successfully used to analyze known and unknown systems, obtaining structural information comparable to X-ray diffraction and standard EXAFS analysis.4–6 In particular, the possibility of performing quantitative analysis on the XANES energy region is very relevant for metallo-protein systems where both the low S/N ratio and the weak scattering power of the light elements surrounding the metal site limit the energy range of the XAS data available for the analysis
We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN
The combination of MXAN analysis and MD simulations1,33 can be a powerful tool to test in detail the classical force fields used in MD because it allows a quantitative comparison between calculation and experimental data

Summary

Introduction

(called Minuit XANes, MXAN)) based on multiple-scattering (MS) theory which is able to extract local structural information around absorbing atoms from experimental XANES data.3 The MXAN method has been successfully used to analyze known and unknown systems, obtaining structural information comparable to X-ray diffraction and standard EXAFS analysis.4–6 In particular, the possibility of performing quantitative analysis on the XANES energy region is very relevant for metallo-protein systems where both the low S/N ratio and the weak scattering power of the light elements surrounding the metal site limit the energy range of the XAS data available for the analysis. We report an iterative application of D-MXAN to the myoglobin protein bonded to carbon monoxide (MbCO) to evaluate the MD force field parameters and, when applicable, to refine them with the twofold objective of allowing a better knowledge of the MbCO structural/dynamic characteristics in solution and producing a more accurate MbCO force field for the community.

Results

Conclusion