Or is the concept inapplicable?
If it were applicable, could statistical mechanical methods apply? Does entropy?
Amino acids in proteins are, of course, not free to move independently like a molecule in solution. First, they are connected to 2 other amino acids (or one other if they are the first or last in the chain, or up to 3 others for a cysteine in a disulfide bond). Second, they are subject to a variety of forces exerted by their surroundings, such as charge-charge interactions, hydrogen bonding, van der Waals interactions, and pi stacking (in the case of aromatic amino acids). Computational methods, particularly molecular dynamics, can be used to model the movement of amino acids in proteins over short time scales.
Amino acids in proteins are, of course, not free to move independently like a molecule in solution. First, they are connected to 2 other amino acids (or one other if they are the first or last in the chain, or up to 3 others for a cysteine in a disulfide bond). Second, they are subject to a variety of forces exerted by their surroundings, such as charge-charge interactions, hydrogen bonding, van der Waals interactions, and pi stacking (in the case of aromatic amino acids). Computational methods, particularly molecular dynamics, can be used to model the movement of amino acids in proteins over short time scales.
Kindly check https://www.hindawi.com/journals/cmmm/2013/197892/
Also check https://www.briancolemd.com/blogpost/2018/12/31/amino-acids-vs-protein-powder/
Thank you for your reference, Mouloud Belachia, most helpful, appreciated, and a good clue to look for articles on small world and proteins in connection with the question posed above, about mean path lengths and proteins.
In a cursory search I found:
(1) Small world network strategies for studying protein structures and binding
Comput Struct Biotechnol J. 2013; 5: e201302006.Published online 2013 Mar 1. doi: 10.5936/csbj.201302006
(2) Yan, W., Zhou, J., Sun, M. et al. The construction of an amino acid network for understanding protein structure and function. Amino Acids 46, 1419–1439 (2014). https://doi.org/10.1007/s00726-014-1710-6
(3) Assessing experimentally derived interactions in a small world
PNAS April 15, 2003 100 (8) 4372-4376; https://doi.org/10.1073/pnas.0735871100
(4) https://www.ebi.ac.uk/training-beta/online/courses/network-analysis-of-protein-interaction-data-an-introduction/
Thanks again, and best regards
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