scholarly journals FF12MC: A revised AMBER forcefield and new protein simulation protocol

2016 ◽  
Vol 84 (10) ◽  
pp. 1490-1516 ◽  
Author(s):  
Yuan‐Ping Pang

2016 ◽  
Author(s):  
Yuan-Ping Pang

ABSTRACTSpecialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheralsp3atom, and (iii) reduced 1-4 interaction scaling factors of torsionsϕandψThis article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left-and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics.



Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 92-100 ◽  
Author(s):  
A. V. Svirid ◽  
◽  
P. V. Ershov ◽  
E. O. Yablokov ◽  
L. A. Kaluzhskiy ◽  
...  


Diabetes ◽  
1991 ◽  
Vol 40 (11) ◽  
pp. 1531-1538 ◽  
Author(s):  
M. B. Davidson ◽  
I. G. Molnar ◽  
A. Furman ◽  
D. Yamaguchi


2019 ◽  
Vol 23 (2) ◽  
pp. 117-119 ◽  
Author(s):  
D. N. Paskalev ◽  
B. T. Galunska ◽  
D. Petkova-Valkova

Tamm–Horsfall Protein (uromodulin) is named after Igor Tamm and Franc Horsfall Jr who described it for the first time in 1952. It is a glycoprotein, secreted by the cells in the thick ascending limb of the loop of Henle. This protein will perform a number of important pathophysiological functions, including protection against uroinfections, especially caused by E. Сoli, and protection against formation of calcium concernments in the kidney. Igor Tamm (1922-1995) is an outstanding cytologist, virologist and biochemist. He is one of the pioneers in the study of viral replication. He was born in Estonia and died in the USA. In 1964 he was elected for a professorship in Rockefeller Institute for Medical Research, where has been working continuously. Since 1959, he became a head of the virology lab established by his mentor and co-author Franc Horsfall. In the course of studies on the natural inhibitor of viral replication, Tamm and Horsfall isolated and characterized biochemically a new protein named after their names. Franc Lappin Horsfall Jr (1906-1971) was a well-known clinician and virologist with remarkable achievements in internal medicine. He was born and died in the USA. He worked in the Rockefeller Hospital from 1934 to 1960, then in the Center for Cancer Research at the Sloan-Kettering Institute. Here he was a leader of a research team studying the molecular mechanisms of immunity, the effects of chemotherapy with benzimidazole compounds (together with I. Tamm), coxsackie viruses, herpes simplex virus, etc. 





2021 ◽  
pp. 100112
Author(s):  
Justin M. Hutchison ◽  
Brooke K. Mayer ◽  
Marcela Vega ◽  
Wambura E. Chacha ◽  
Julie L. Zilles


2007 ◽  
Vol 63 (a1) ◽  
pp. s137-s137
Author(s):  
T. Hasegawa ◽  
K. Hamada ◽  
M. Sato ◽  
M. Motohara ◽  
S. Sano ◽  
...  


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexandra Siklitskaya ◽  
Ewelina Gacka ◽  
Daria Larowska ◽  
Marta Mazurkiewicz-Pawlicka ◽  
Artur Malolepszy ◽  
...  

AbstractGraphene-based nanohybrids are good candidates for various applications. However, graphene exhibits some unwanted features such as low solubility in an aqueous solution or tendency to aggregate, limiting its potential applications. On the contrary, its derivatives, such as graphene oxide (GO) and reduced graphene oxide (RGO), have excellent properties and can be easily produced in large quantities. GO/RGO nanohybrids with porphyrins were shown to possess great potential in the field of photocatalytic hydrogen production, pollutant photodegradation, optical sensing, or drug delivery. Despite the rapid progress in experimental research on the porphyrin-graphene hybrids some fundamental questions about the structures and the interaction between components in these systems still remain open. In this work, we combine detailed experimental and theoretical studies to investigate the nature of the interaction between the GO/RGO and two metal-free porphyrins 5,10,15,20-tetrakis(4-aminophenyl) porphyrin (TAPP) and 5,10,15,20-tetrakis(4-hydroxyphenyl) porphyrin (TPPH)]. The two porphyrins form stable nanohybrids with GO/RGO support, although both porphyrins exhibited a slightly higher affinity to RGO. We validated finite, Lerf–Klinowski-type (Lerf et al. in J Phys Chem B 102:4477, 1998) structural models of GO ($$\hbox {C}_{59}\hbox {O}_{26}\hbox {H}_{26}$$ C 59 O 26 H 26 ) and RGO ($$\hbox {C}_{59}\hbox {O}_{17}\hbox {H}_{26}$$ C 59 O 17 H 26 ) and successfully used them in ab initio absorption spectra simulations to track back the origin of experimentally observed spectral features. We also investigated the nature of low-lying excited states with high-level wavefunction-based methods and shown that states’ density becomes denser upon nanohybrid formation. The studied nanohybrids are non-emissive, and our study suggests that this is due to excited states that gain significant charge-transfer character. The presented efficient simulation protocol may ease the properties screening of new GO/RGO-nanohybrids.



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