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286534 occurrences (No.87 in the rank) during 5 years in the PubMed. [no cache] 500 found

313) Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms.

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PMID:34575064 DOI:10.3390/life11090915

2021 Life (Basel, Switzerland)

* Evolution of Thyroglobulin Loop Kinetics in EpCAM.

- Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

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(1)172 of	(10)5 that	(19)3 step	(28)2 increased
(2)40 and	(11)5 the	(20)2 (ESR),	(29)2 it
(3)32 was	(12)4 (HR),	(21)2 (RMR)	(30)2 lactate,
(4)31 null	(13)4 among	(22)2 after	(31)2 or
(5)24 in	(14)4 discrimination	(23)2 at	(32)2 respiratory
(6)8 variability	(15)4 is	(24)2 attributable	(33)2 to
(7)6 constants	(16)4 were	(25)2 between	(34)2 top
(8)6 for	(17)3 enzyme	(26)2 constant	(35)2 which
(9)5 (HR)	(18)3 on	(27)2 equations

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--- WordNet output for rate --- =>価格を評定する, 割合, 率, 歩合, 料金, 値段, 相場, 速度, 度合, 人を〜を思う, みなす, 価値がある, 人を〜とみなす, 科金, 評価する Overview of noun rate The noun rate has 4 senses (first 3 from tagged texts) 1. (68) rate -- (a magnitude or frequency relative to a time unit; "they traveled at a rate of 55 miles per hour"; "the rate of change was faster than expected") 2. (39) rate, charge per unit -- (amount of a charge or payment relative to some basis; "a 10-minute phone call at that rate would cost $5") 3. (1) pace, rate -- (the relative speed of progress or change; "he lived at a fast pace"; "he works at a great rate"; "the pace of events accelerated") 4. rate -- (a quantity or amount or measure considered as a proportion of another quantity or amount or measure; "the literacy rate"; "the retention rate"; "the dropout rate") Overview of verb rate The verb rate has 3 senses (first 3 from tagged texts) 1. (9) rate, rank, range, order, grade, place -- (assign a rank or rating to; "how would you rank these students?"; "The restaurant is rated highly in the food guide") 2. (2) rate -- (be worthy of or have a certain rating; "This bond rates highly") 3. (1) rate, value -- (estimate the value of; "How would you rate his chances to become President?"; "Gold was rated highly among the Romans") --- WordNet end ---