TUPÃ: Electric field analyses for molecular simulations

Abstract

We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/.

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

“…Intrigued by the well-defined global free energy minimum at the S3 binding site in both systems, we investigated the electrostatic forces stabilizing the binding of K + ions. To this end, we employed TUPÃ to calculate the electric fields ( E⃗ ) exerted by the GQs across their O6-core axis for unbound states (snapshots with no bound K + bound at S1 or S3, Figure ). To facilitate our analysis, we aligned the O6-core axis to the Cartesian z -axis, and the plane formed by C1′ atoms of T2 was used to define z = 0.…”

Designed Local Electric Fields─Promising Tools for Enzyme Engineering

“…Various codes to automatically compute local electric fields based on the output of (QM/MM) calculations, as well as their alignment with specific bonds and/or the reaction axis have been developed over the years. Two open-source and user-friendly Python implementations are TITAN and TUPA . TITAN takes as input either an abstract point charge distribution, an AMBER- or CHARMM-compatible PDB file, or a GAUSSIAN09 log file containing a natural bond order (NBO) analysis, as well as an additional input file specifying the charges/atoms/residues of interest as well as the evaluation point and reaction/bond axis, and outputs the intensity, as well as the components along the specified axes, of the electric field .…”

“…TUPA has similar capabilities but is more tailored toward MD analyses. It enables among others the automated calculation of an electric field across all timeframes of an MD simulation, facilitating an analysis of the temporal evolution of the field exerted at the (active) site of interest …”

A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient

“…The TITAN and TUP Ã codes were used to quantify the local electric elds (LEFs) present in the systems. 22,62,63 Using the TUP Ã code, we quantied the evolution of LEFs for solvated cage, oxidant HM1 & entire system from whole MD simulation trajectory at 10 ps time intervals, along the reaction axis, (z-axis, Fe]O) as well as the selectivity axis (y-axis). The solvent molecules present in the 3 Å vicinity of HM1 were included.…”