chemstructo

Scientists and science enthusiasts in the fields of #structuralbiology, #biochemistry, #chemistry, #physics, #biology, and #drugdiscovery.

[chemstructo @chemstructo]

Normal mode of the beta-2-adrenoceptor (PDB: 5x7d) showing some of the possible global dynamics of this protein

#science #molecularmodelling #dynamics #protein #scicomm #sciart #phd #postdoc #biochemistry #gpcr #chemistry #lifescience #biology #structuralbiology

[chemstructo @chemstructo]

Elastic Network Model (ENM) for the beta-2-adrenergic receptor.
This type of coarse-grained model is a simple way of exploring protein structural dynamics
PDB used: 5x7d
#science #scicomm #biochemistry #chemistry #biology #lifescience #phd #postdoc #sciart #molecularmodelling

[chemstructo @chemstructo]

Reaction between carbon dioxide and hydroxide ion via semiempirical QM method using water solvation model.
One method for carbon capture is by "wet-scrubbing" air with an alkaline solution.

#science #scicomm #chemistry #phd #postdoc #carbon #molecularmodelling #quantumchemistry

[chemstructo @chemstructo]

Top 10 binding poses from molecular docking of the drug Venetoclax to its target protein, Bcl-2 Venetoclax promotes apoptosis (programmed cell death) of certain types of cancer cells PDB: 6o0k #science #drugdiscovery #scicomm #phdlife #biochemistry #chemistry #PhD #postdoc

[chemstructo @chemstructo]

In situ molecular dynamics of the drug venetoclax in the binding site of its target protein, Bcl-2.
Protein atoms were fixed to see how the ligand explores the experimentally determined binding pocket.
#science #scicomm #sciart #drugdiscovery #chemistry #biochemistry #lifescience

[chemstructo @chemstructo]

X-Ray crystal structure (PDB: 1HZH) of an immunoglobulin G (Ig G) antibody that targets and neutralizes an HIV antigen

Reference: (2001) Science 293: 1155-1159

#structuralbiology #science #antibody #scicomm #sciart #biochemistry #chemistry #phd #postdoc #lifescience #molecule

[chemstructo @chemstructo]

Molecular docking of the inverse-agonist carazolol (colored in magenta) to the β2 adrenoreceptor (PDB: 5X7D). Top three docked poses are shown in relation to the crystallized ligand (which is shown midway through the video).

#science #scicomm #sciart #docking #chemistry #PhD

[chemstructo @chemstructo]

The structure of Human olfactory receptor OR51E2 was recently solved (PDB: 8F76) by cryo-EM, and it is one of ~400 related receptors that are involved in our sense of smell (olfaction).

Reference: (2023) Nature 615: 742-749

#science #structuralbiology #biochemistry #chemistry

[chemstructo @chemstructo]

Molecular dynamics simulation for folding of the 10-residue peptide, Chignolin. Implicit solvation.

#chemistry #moleculardynamics #modelling #science #biochemistry #lifescience #proteinfolding #dynamics #phd #postdoc #phdlife #postdoclife #sciart #scicomm #molecule #molecular

[chemstructo @chemstructo]

Formation of calcium carbonate complex from the free carbonate and calcium ions.
Optimization via semi-empirical QC with water solvation model.

#chemistry #quantumchemistry #modelling #science #biochemistry #lifescience #materialsscience #phd #postdoc

[chemstructo @chemstructo]

X-Ray structure of a segment of DNA (PDB: 1BNA)

Ref: (1981) Proc Natl Acad Sci U S A 78: 2179-2183
#structuralbiology #chemistry #biochemistry #lifescience #phd #postdoc #biology #scicomm #sciart

[chemstructo @chemstructo]

Walden inversion reaction between hydroxide and chloromethane. A classic example of an SN2 nucleophilic substitution reaction.
Semi-empirical quantum chemical optimization used to model this reaction.

#science #chemistry #phd #postdoc #scicomm #sciart #biochemistry #compchem

[chemstructo @chemstructo]

C240 Fullerene shown with delocalized electrons.
Amazing that fullerenes can actually be found in nature!

#science #scicomm #sciart #chemistry #phd #postdoc

[chemstructo @chemstructo]

Tag cloud (word cloud) showing prevalence of author last name in articles published in Nature with "NMR" in the title or abstract.

#scicomm #sciart #nmrspectroscopy #lifescience #postdoc #phd #biochemistry #structuralbiology #chemistry

[chemstructo @chemstructo]

Semi-empirical quantum chemical geometry optimization of a histidine-porphyrin complex.
Note the formation of the bond between the central iron and the histidine nitrogen.

#science #chemistry #biochemistry #sciart #scicomm #quantumchemistry #computationalchemistry #phd #postdoc

[chemstructo @chemstructo]

Rat liver vault particle (PDB: 4V60).

Reference: (2009) Science 323: 384-388

#science #sciart #scicomm #chemistry #biochemistry #biology #xraycrystallography #phd #postdoc #lifescience

[chemstructo @chemstructo]

Buckminsterfullerene (C60).
Bond orders shown as delocalized electrons.

#science #chemistry #phd #postdoc #scicomm #sciart

[chemstructo @chemstructo]

Sampling of different bound conformations of ATP in the binding site of Ribonuclease A using Monte Carlo approach.
Note that the receptor (RNase) was fixed and only the ligand was allowed to sample different conformations.

PDB:2W5I used in the simulation.

[chemstructo @chemstructo]

In vacuo semi-empirical quantum chemical optimization of lysine.

Plot shows the system energy with each optimization step until convergence.

[chemstructo @chemstructo]

A beta-Lactamase In Complex With Benzylpenicillin (PDB:1IYQ).

Ref: (2002) J Biol Chem 277: 46601-46608

#structuralbiology #drugdiscovery #scicomm #phd #postdoc #chemistry #biochemistry