StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions

Abstract

Studying biomolecular interactions is a crucial but challenging task. Due to their large scales, many biomolecular interactions are difficult to be simulated via all atom models. An effective approach to investigate the biomolecular interactions is highly demanded in many areas. Here we introduce a Structure Manipulation (StructureMan) program to operate the structures when studying the large-scale biomolecular interactions. This novel StructureMan tool provides comprehensive operations which can be utilized to study the interactions in various large biological systems. Combining with electrostatic calculation programs such as DelPhi and DelPhiForce, StructureMan was implemented to reveal the detailed electrostatic features in two large biological examples, the viral capsid and molecular motor-microtubule complexes. Applications on these two examples revealed interesting binding mechanisms in the viral capsid and molecular motor. Such applications demonstrated that the StructureMan can be widely used when studying the biomolecular interactions in large scale biological problems. This novel tool provides an alternative approach to efficiently study the biomolecular interactions, especially for large scale biology systems. The StructureMan tool is available at our website: http://compbio.utep.edu/static/downloads/script-for-munipulation2.zip.

Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2

“…Electrostatic forces of SARS-CoV and SARS-CoV-2 N proteins’ RBDs with RNAs at distances from 5 Å to 40 Å with a step size of 5 Å were separated by StructureMan [ 32 ] and calculated by DelPhiForce at each position (see Figure 5 ). The directions of the blue arrows are illustrated to show the directions of net forces between N proteins and RNAs.…”

“…Their surfaces were visualized by Chimera [ 31 ] using the color scale range from −1.0 to 1.0 kT/e (see Figure 1 ). In order to compare the directions and strengths of electrostatic forces, the N protein and RNA was separated from 5 Å to 40 Å with the step size of 5 Å using StructureMan [ 32 ]. Then at each position, the electrostatic force was calculated by DelPhiForce.…”

Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin

“…After the calculation, the values of electrostatic potential on the surface were visualized with Chimera (Figure 3). In order to visualize electric field lines between kinesin and tubulins and to get the best visualization, we separated the alpha tubulin and the beta tubulin by 20 Å using StructureMan [37], and the separated kinesin from them(the separated tubulins) by 20 Å. VMD was implemented based on the electrostatic potential map from DelPhi calculations and the color scale range was set from −3.0 to 3.0 kT/e. The results of electrostatic potetial calculation are shown in Figures 3 and 4, and the visuialization of electric field lines are shown in Figures 5 and 6.…”

The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2

“…With the fast developments of computing technology, computational methods have been widely used in drug-related research [12], including protein-protein interactions [13,14], MD simulations [15], coarse-grained models [16], pH dependence of protein-protein interactions [17][18][19][20], etc. Our previous studies have applied multi-scale computational methods to study several pathogens [21][22][23][24][25] including the SARS-CoV-2 viruses [26,27], which revealed some mechanisms of the SARS-CoV-2 S protein. Additionally, many other research groups have made successful progress to understand the SARS-CoV-2 using computational methods [28,29].…”