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• W2431609975 endingPage "11242" @default.
• W2431609975 startingPage "11229" @default.
• W2431609975 abstract "The human cluster determinant 4 (CD4), expressed primarily on the surface of T helper cells, serves as a coreceptor in T-cell receptor recognition of MHC II antigen complexes. Besides its cellular functions, CD4 serves as a primary receptor of human immunodeficiency virus (HIV) type 1. The cytoplasmic tail of CD4 (residues 402-419) is known to be involved in direct interaction with the HIV-1 proteins Vpu and Nef. These two viral accessory proteins (Vpu and Nef) downregulate CD4 in HIV-1 infected cells by multiple strategies and make the body susceptible to all forms of infections. In this work, we carried out extensive replica exchange molecular dynamics simulations in explicit water with three popular protein force fields Amber ff99SB, Amber ff99SB*-ILDN, and CHARMM36 to characterize the equilibrium conformational ensemble of CD4-tail (402-419) and further validated the simulated ensembles with known NMR data. We found that ff99SB*-ILDN gives a better description of the structural ensemble of this peptide compared with ff99SB and CHARMM36. The peptide adopts multiple distinct conformations with varying degree of residual secondary structures. In particular, we observed 28, 7, and 5% average α-helical, β-strand, and 3(10)-helix content, respectively, for ff99SB*-ILDN. The peptide chain shows the tendency of helix formation in a cooperative manner, seeding at residues 407-410, and subsequently extending toward both ends of the chain. Furthermore, we constructed Markov state model (MSM) from large-scale molecular dynamics simulations to study the dynamics of transitions between different metastable states explored by this peptide. The mean first passage times computed from MSM indicate rapid interconversion of these states, and the time scales of transitions range from several nanoseconds to hundreds of microseconds. Our results show good agreement with experimental data and could help to understand the key molecular mechanisms of T-cell activation and HIV-mediated receptor interference." @default.
• W2431609975 created "2016-06-24" @default.
• W2431609975 creator A5002919238 @default.
• W2431609975 creator A5075032133 @default.
• W2431609975 creator A5091554974 @default.
• W2431609975 date "2015-07-15" @default.
• W2431609975 modified "2023-09-25" @default.
• W2431609975 title "Structural Ensemble of CD4 Cytoplasmic Tail (402–419) Reveals a Nearly Flat Free-Energy Landscape with Local α-Helical Order in Aqueous Solution" @default.
• W2431609975 cites W1588488170 @default.
• W2431609975 cites W1621734805 @default.
• W2431609975 cites W1785994082 @default.
• W2431609975 cites W1847426433 @default.
• W2431609975 cites W1963569988 @default.
• W2431609975 cites W1965418299 @default.
• W2431609975 cites W1966078827 @default.
• W2431609975 cites W1969256423 @default.
• W2431609975 cites W1973243106 @default.
• W2431609975 cites W1973264045 @default.
• W2431609975 cites W1976499671 @default.
• W2431609975 cites W1976821598 @default.
• W2431609975 cites W1977626220 @default.
• W2431609975 cites W1977863518 @default.
• W2431609975 cites W1977969550 @default.
• W2431609975 cites W1979070806 @default.
• W2431609975 cites W1980146626 @default.
• W2431609975 cites W1981164507 @default.
• W2431609975 cites W1984266461 @default.
• W2431609975 cites W1985070997 @default.
• W2431609975 cites W1988091837 @default.
• W2431609975 cites W1990070794 @default.
• W2431609975 cites W1991820295 @default.
• W2431609975 cites W1994454005 @default.
• W2431609975 cites W2004508024 @default.
• W2431609975 cites W2006192061 @default.
• W2431609975 cites W2007922771 @default.
• W2431609975 cites W2008708467 @default.
• W2431609975 cites W2011788545 @default.
• W2431609975 cites W2012029966 @default.
• W2431609975 cites W2014759070 @default.
• W2431609975 cites W2016267980 @default.
• W2431609975 cites W2020055566 @default.
• W2431609975 cites W2023921624 @default.
• W2431609975 cites W2025899185 @default.
• W2431609975 cites W2027255849 @default.
• W2431609975 cites W2027740448 @default.
• W2431609975 cites W2035165231 @default.
• W2431609975 cites W2035266068 @default.
• W2431609975 cites W2035443421 @default.
• W2431609975 cites W2037159954 @default.
• W2431609975 cites W2040809566 @default.
• W2431609975 cites W2046223820 @default.
• W2431609975 cites W2046285452 @default.
• W2431609975 cites W2047545214 @default.
• W2431609975 cites W2056723350 @default.
• W2431609975 cites W2057477511 @default.
• W2431609975 cites W2061144516 @default.
• W2431609975 cites W2065281489 @default.
• W2431609975 cites W2066795144 @default.
• W2431609975 cites W2067174909 @default.
• W2431609975 cites W2067680762 @default.
• W2431609975 cites W2072659663 @default.
• W2431609975 cites W2075243501 @default.
• W2431609975 cites W2080574127 @default.
• W2431609975 cites W2085213650 @default.
• W2431609975 cites W2085567137 @default.
• W2431609975 cites W2086264258 @default.
• W2431609975 cites W2087729059 @default.
• W2431609975 cites W2088647884 @default.
• W2431609975 cites W2093250120 @default.
• W2431609975 cites W2093416018 @default.
• W2431609975 cites W2096125044 @default.
• W2431609975 cites W2097891553 @default.
• W2431609975 cites W2100736103 @default.
• W2431609975 cites W2102345899 @default.
• W2431609975 cites W2103945336 @default.
• W2431609975 cites W2109154308 @default.
• W2431609975 cites W2111339528 @default.
• W2431609975 cites W2113282092 @default.
• W2431609975 cites W2118608964 @default.
• W2431609975 cites W2120595908 @default.
• W2431609975 cites W2129213941 @default.
• W2431609975 cites W2132589721 @default.
• W2431609975 cites W2132720084 @default.
• W2431609975 cites W2136941426 @default.
• W2431609975 cites W2141796022 @default.
• W2431609975 cites W2144288821 @default.
• W2431609975 cites W2144975103 @default.
• W2431609975 cites W2158476854 @default.
• W2431609975 cites W2161605421 @default.
• W2431609975 cites W2168781610 @default.
• W2431609975 cites W2169693347 @default.
• W2431609975 cites W2171268876 @default.
• W2431609975 cites W2292301738 @default.
• W2431609975 cites W2313338745 @default.
• W2431609975 cites W2318815774 @default.
• W2431609975 cites W2319226565 @default.
• W2431609975 cites W2325642794 @default.
• W2431609975 cites W2332848601 @default.

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