What does it mean by "terminally blocked" amino acid residue?

* [Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method](https://pubmed.ncbi.nlm.nih.gov/11948589/)



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> For local interaction energy, use is made of a two-dimensional Fourier series expansion of the energies of model **terminally blocked** amino acid residues, calculated with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field in the angles lambda(1) and lambda(2) defining the rotation of peptide groups adjacent to a C-alpha carbon atom about the corresponding C-alpha ...C-alpha virtual-bond axes.
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What does it mean by **terminally blocked** amino acid residue?




If the protein is an open chain, the amino acids it consists of either are be *within* the chain, and enclosed by other amino acids. Or they are at either one of the termini of the chain; hence C-terminus about the carboxy group, or N-terminus relating to the amino group.


Further on, their amino and carboxy group either may by accessible ("open") to further reaction with an other additional amino acid, or e.g., a BOC group protects ("closes") the amine to establish a link with an other.


Hence, *terminally blocked* refers to the uncoiled protein chain, unable to to bind to additional amino acids *via the chain's* amino or carboxy group. It doesn't state if some of the R in the side chains still may get in touch with an other side chain which can be intra-, or intermolecular (e.g. cysteine vs cystine).


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