We have recently applied molecular modeling and simulation techniques to construct an atomic model of the TM part of a connexon, based on published Cα scaffold [11].
A common approach to infer atomic detail about conformational changes is to construct an atomic model consistent with the low-resolution data, using known X-ray structures.
12– 15 In light of the known structural information of skeletal muscle thin filament, we have constructed an atomic model of cardiac thin filament in blocked and closed states by using an integrative template-based modelling approach.
The molecular dynamics method, which is different from continuous mechanics is employed to investigate the features of machining energy dissipation, cutting force and stress state, and constructs an atomic model of the tool and the work piece, and explains the microscale mechanism of material remove and surface generation of nanometer (subnanometer) manufacturing.
The atomic details of termination complexes have not been fully elucidated in crystal structures and are sufficiently complex that constructing a credible atomic model for a termination intermediate would present significant challenges.
This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1–RC–PufX dimers & 2 RC–LH1–PufX monomers, 4 cytbc1 dimers and 2 ATP synthases.
Using the average density of amorphous carbon, an atomic model corresponding to a 100 × 100 × 100 Å carbon cell was constructed and used for image simulation with various settings for slice thickness and pixel sampling.
In order to construct a full, atomic model of the interface for use in image simulation, it is necessary to characterize its structure through an analysis technique such as atomic packing density profiles (aka probability density distributions, or PDDs).
We used the MDFF package (Trabuco et al., 2008) to develop an atomic model for our ATP analog map, starting with the crystal structure of the same chemical state of the same kinesin construct co-complexed with a tubulin dimer (Gigant et al., 2013).
