<aside> 👥 Author: Mukundh Murthy, Michael Trinh Contributors: Alston Lo, Rikard Saqe, Subaita Rahman, Seyone Chithrananda


<aside> 🔥 Guests this Month: Post Doc: TBD PI: TBD


Computational Chemistry: A Bird’s Eye View

The proteins that carry out nature's processes in our healthy bodies and in disease are enormously complex. To understand something as complicated as a protein, we start by uncovering its structure and its basic function.

There's a simple principle in biology: function arises from shape. The structure of a protein determines how it functions: both in terms of binding to other proteins and processing small molecule inputs.

Proteins rarely act alone in any situation, as is the case of enzymes that catalyze reactions between small molecules. The enzymes themselves are proteins, but their chemical inputs (substrates) and outputs (products) are simple, nimble small molecules.

Core Concepts in Computational Chemistry

Protein Folding Problem

The structure of a simple protein contains 3 layers of complexity, while more complicated proteins contain an additional 4th layer of complexity.

Primary Structure (1st Layer): A string of amino acids, the polypeptide chain. Made from 20 different types of amino acids, each of which has different sizes, molecular weight, chemical properties, and unique behavior under specific reaction conditions.

We often denote a polypeptide chain in text by abbreviating its amino acid sequence:

Secondary Structure (2nd layer): The small-scale folding of the polypeptide chain. Amino acids in nearby positions will fold and bind on one another to give basic sub-structures to the protein: alpha helixes, beta-sheets. (ex. His 5 ↔ Glu 8)


PC: Immune Foundation

3rd layer: Large-scale folding of the basic sub-structures to form larger motifs that give the protein its functional form. Some of these structures include coiled coils, alpha bundles, hairpins, greek keys, Beta-barrels, and simple proteins. (ex. Asp 45 ↔ Arg 80)


PC: Pearson, Principles of Biochemistry

4th layer: Grouping of multiple protein domains into a functioning polyprotein or complex protein.