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A protein is a biological molecule made of one or more polypeptide chains: ordered amino acid residues joined by peptide bonds. Biological translation assembles a chain in the order specified by messenger RNA codons. Protein folding then brings parts of that chain into spatial relationships that support its function. See Cooper, The Cell: protein composition and structure. These processes can overlap in a biological cell; the sequence-to-shape explanation does not require waiting until biological translation finishes before any folding begins. See Cooper, The Cell: protein folding and processing.

The useful connection is from information to physical work. A protein's protein primary structure records an order; its protein tertiary structure can bring distant amino acid residues together at an active site. An enzyme uses such an arrangement to recognize a substrate and accelerate a chemical reaction. Other proteins serve as receptors, membrane transport proteins or structural material. For example, actin assembles into filaments whose mechanical properties can be described by biopolymer mechanics. See Alberts et al., Molecular Biology of the Cell: protein function and binding.

Order matters beyond composition. Let A stand for alanine and M for methionine, and read from the N-terminus to the C-terminus. The illustrative strings AMAMAMAMAMAM and AAAAAAMMMMMM each contain exactly six A and six M amino acid residues. Each has $12-1=11$ peptide bonds when made into one unbranched polypeptide chain. In the first string all eleven neighboring pairs have different letters; in the second only the pair at positions 6 and 7 does. A composition histogram therefore loses information about which amino acid residues are neighbors. Their arrangements can affect protein folding and function; these short invented strings neither specify a known functional protein nor establish what shape either would adopt.

Protein structure is a moving arrangement, not a permanently rigid outline. Substrate binding can change an enzyme's shape through induced fit, and a functional protein can include flexible regions. Sequence, surroundings and interacting molecules must therefore be considered together. See Alberts et al.: binding, conformational changes and protein function.

A fluorescence readout of actin assembly using polymerization-dependent signal from a labelled actin fraction. Label effects, direct fluorescence changes, quenching and background must be controlled.^[ref]

A small GTPase participating in protrusion and polarity in migrating cells.

Nucleotide exchange changes recruitment of effectors that regulate the actin cytoskeleton. Spatially restricted activity can help select a protrusive region, connecting a biochemical switch to directional cell movement. ^[ref]

A small GTPase that promotes actin assembly and myosin regulation during contractile-ring formation and other cellular processes.

Rickettsia parkeri is a spotted-fever-group intracellular bacterium used to study Sca2-dependent actin assembly. Its motility machinery should not be generalized to every rickettsial species.

Postmortem muscular stiffening associated with loss of sufficient ATP to maintain normal detachment of actin–myosin cross-bridges. It is distinct from freezing and heat coagulation.

Sandrine De Seranno investigated signalling between vascular endothelial cells and glial cells in the neuroendocrine brain. A 2004 study combined purified rat median eminence endothelial cells with cultured tanycytes, identifying nitric oxide-dependent changes in the actin cytoskeleton.^[ref]

Electron microscopy complemented the culture manipulation: stimulating endogenous nitric oxide release changed how glial endings and GnRH-containing axons approached the vascular surface. The work connected a diffusible signal with altered cellular geometry at a neurovascular interface.^[ref]

In 1997, Hiroyuki Noji and colleagues attached a fluorescent actin filament to the central $\gamma$ shaft of isolated $F_1$. With ATP supplied, the marker made sustained rotations. This exposed rotation directly, but used ATP hydrolysis: there was no membrane $F_0$ motor producing ATP from a proton-motive force in this assay.^[ref]

A subsequent primary experiment made the optical readout much faster. Purified Escherichia coli $F_1$ was immobilized on glass in a $30\mu \mathrm{m}$-deep flow cell, with a $60\mathrm{nm}$ gold bead attached to $\gamma$. With $2\mathrm{mM}$ ATP and magnesium supplied, laser illumination and dark-field microscopy recorded bead positions at $4000$ or $8000$ frames per second. The position trajectory resolved turns and intervening dwells. This apparatus follows a shaft-attached marker, rather than imaging the shaft's chemical atoms.^[ref]

Controls addressed perturbation and chemical activity: comparison of $40$–$200\mathrm{nm}$ probes found similar rates for the two smallest sizes, supporting low drag; a separate coupled-enzyme assay followed ATP hydrolysis through NADH absorbance. But the rotational analysis excluded pauses longer than $0.1\mathrm{s}$, so it characterizes continuously active intervals, not total output including long inhibited periods. It neither counts transported protons nor measures simultaneous single-molecule ATP synthesis.^[ref]

The experimental distinction is essential. Sustained directional marker motion tests a rotary mechanism. Demonstrating proton-driven synthesis additionally requires intact $F_0{F}_1$ in a membrane with a controlled proton-motive force and a chemical ATP-production readout; dependence on that driving force and inhibition or respiratory uncoupling controls then test the proposed energy coupling. A rotation movie alone cannot establish the complete material and free energy ledger.

Spectrin is a flexible cytoskeletal protein that forms a meshwork beneath the cell membrane, often through assemblies of alpha and beta chains. Connections to membrane-associated components and actin help distribute mechanical stress. The red blood cell provides a striking example: its membrane skeleton supports repeated deformation through narrow vessels. Spectrin is also present in other cells, where related assemblies help organize membrane domains. ^[ref]

Researcher in localized translation. Hüttelmaier and collaborators investigated Src-dependent phosphorylation of ZBP1 in control of beta-actin translation, connecting a signaling event with where a protein is synthesized.^[ref]

A tanycyte is a specialized ependymal cell and glial cell of the hypothalamus. Its body can line the third ventricle, while a long process extends toward underlying tissue. In the median eminence, tanycytic endings surround neurosecretory terminals near blood vessels.^[ref]

In cultured rat tanycytes, signals from endothelial cells altered actin organization through nitric oxide.^[ref]

This supplies an illuminating example of structural regulation: a glial cell can change the geometry around a neuron's ending without changing the ending's identity. Evidence for one such interaction does not establish identical functions for every tanycyte subtype.

A filament-associated regulatory protein whose position along actin helps control myosin access. In skeletal muscle its coupling to troponin connects calcium regulation to cross-bridge activity.

A calcium-responsive regulatory protein complex on thin muscle filaments. Changes in its occupancy and conformation couple calcium signals to movement of tropomyosin and accessibility of myosin-binding sites on actin.

vinculin is an adhesion-associated protein that can bind exposed regions of talin and contribute to coupling adhesions to actin. Recruitment and load depend on the state of the surrounding linkage.

A Western blot loading control estimates lane-to-lane sample differences. A reference protein, such as actin, must have stable abundance and detection responsive to amount. Equal saturated bands fail to establish equal loading. ^[ref]