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The Young's modulus of a single protein can be found through molecular dynamics simulation. Using either atomistic force-fields, such as CHARMM or GROMOS, or coarse-grained forcefields like Martini, [121] a single protein molecule can be stretched by a uniaxial force while the resulting extension is recorded in order to calculate the strain.
Several protein residues can be methylated, most notably the positive groups of lysine and arginine. Arginine residues interact with the nucleic acid phosphate backbone and commonly form hydrogen bonds with the base residues, particularly guanine, in protein–DNA complexes. Lysine residues can be singly, doubly and even triply methylated.
Protein structures range in size from tens to several thousand amino acids. [2] By physical size, proteins are classified as nanoparticles, between 1–100 nm. Very large protein complexes can be formed from protein subunits. For example, many thousands of actin molecules assemble into a microfilament.
This can be done in terms of the chemical elements present, or by molecular structure e.g., water, protein, fats (or lipids), hydroxyapatite (in bones), carbohydrates (such as glycogen and glucose) and DNA. In terms of tissue type, the body may be analyzed into water, fat, connective tissue, muscle, bone, etc.
Once the protein is produced, it can then fold to produce a functional three-dimensional structure. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein complex. In prokaryotes each ribosome is composed of small (30S) and large (50S) components, called subunits, which are bound to each other:
The endoplasmic reticulum is also part of a protein sorting pathway. It is, in essence, the transportation system of the eukaryotic cell. The majority of its resident proteins are retained within it through a retention motif. This motif is composed of four amino acids at the end of the protein sequence.
Collagen is the most abundant protein in the ECM, and is the most abundant protein in the human body. [ 17 ] [ 18 ] It accounts for 90% of bone matrix protein content. [ 19 ] Collagens are present in the ECM as fibrillar proteins and give structural support to resident cells.
Myoglobin is found in Type I muscle, Type II A, and Type II B; although many older texts describe myoglobin as not found in smooth muscle, this has proved erroneous: there is also myoglobin in smooth muscle cells. [14] Myoglobin was the first protein to have its three-dimensional structure revealed by X-ray crystallography. [15]