Markus Meuwly

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A new computational approach is proposed to probe the importance of residue side chains for the stability of a protein fold. Computational mutations to estimate protein stability (CMEPS) is based on the notion that the binding free energy corresponding to the complexation of a given side chain, considered as a "pseudo-ligand" of the wild type protein,(More)
The rebinding of CO to myoglobin (Mb) from locations around the active site is studied using a combination of molecular dynamics and stochastic simulations for native and L29F mutant Mb. The interaction between the dissociated ligand and the protein environment is described by the recently developed fluctuating three-point charge model for the CO molecule.(More)
Neuroglobin (Ngb) belongs to the large family of globular heme proteins capable of binding small gaseous ligands such as O(2), CO, or NO within their active site. In this work, we have analyzed CO migration pathways in photolyzed NgbCO using molecular dynamics (MD) simulations in combination with Fourier transform infrared temperature derivative(More)
The structural origins of infrared absorptions of photodissociated CO in murine neuroglobin (Ngb) are determined by combining Fourier transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations. Such an approach allows to identify and characterize both the different conformations of the Ngb active site and the transient ligand docking(More)
The influence of electrostatic multipole moments up to hexadecapole on the dynamics of photodissociated carbon monoxide (CO) in myoglobin is investigated. The CO electrostatic potential is expressed as an expansion into atomic multipole moments of increasing order up to octopole which are obtained from a distributed multipole analysis. Three models with(More)
The description of molecular systems using multipolar electrostatics calls for automated methods to fit the necessary parameters. In this paper, we describe an open-source software package that allows fitting atomic multipoles (MTPs) from the ab initio electrostatic potential by adequate atom typing and judicious assignment of the local axis system. By(More)
In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme protein, the sperm whale myoglobin double mutant L29W-S108L, and its dependence on temperature from 20 to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the(More)
Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The(More)
Currently, all standard force fields for biomolecular simulations use point charges to model intermolecular electrostatic interactions. This is a fast and simple approach but has deficiencies when the electrostatic potential (ESP) is compared to that from ab initio methods. Here, we show how atomic multipoles can be rigorously implemented into common(More)
Three-legged piano stool complexes are prototypical organometallic complexes relevant to a wide range of chemically relevant questions. Force field parametrization of transition-metal complexes is difficult and underdeveloped, and metal-specific force fields and software are required. Here we report our efforts to derive parameters for the conventional(More)