Uncovering allostery and regulation in SAMHD1 through molecular dynamics simulations.
The human sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a retroviral restriction factor in myeloid cells and non-cycling CD4+ T cells, a feature imputed to its phosphohydrolase activity-the enzyme depletes the cellular dNTP levels inhibiting reverse transcription. The functionally active form of SAMHD1 is an allosterically triggered tetramer which utilizes GTP-Mg+2-dNTP cross bridges to link and stabilize adjacent monomers. However, very little is known about how it assembles into a tetramer and how long the tetramer stays intact. In this computational study, we provide a molecular dynamics based analysis of the structural stability and allosteric site dynamics in SAMHD1. We have investigated the allosteric links which assemble and hold the tetramer together. We have also extended this analysis to a regulatory mutant of SAMHD1. Experimental studies have indicated that phosphorylation of T592 downregulates HIV-1 restriction. A similar result is also achieved by a phosphomimetic mutation T592E. While a mechanistic understanding of the process is still elusive, the loss of structural integrity of the enzyme is conjectured to be the cause of the impaired dNTPase activity of the T592E mutant. MD simulations show that the T592E mutation causes slightly elevated local motions which remain confined to the short helix (residues 591-595), which contains the phosphorylation site and do not cause long-range destabilization of the SAMHD1 tetramer within the timeframe of the simulations. Thus, the regulatory mechanism of SAMHD1 is a more subtle mechanism than has been previously suspected. Proteins 2017; 85:1266-1275. © 2017 Wiley Periodicals, Inc.
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India, 400076.
Kajwal Kumar
KK
Patra
Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229-3900.
Akash
A
Bhattacharya
Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India, 400076.
Swati
0000-0003-1960-443X
S
Bhattacharya
D000494:Allosteric Regulation; D000495:Allosteric Site; D019943:Amino Acid Substitution; D003838:Deoxyadenine Nucleotides / Q000737:chemistry* / Q000378:metabolism; D018698:Glutamic Acid / Q000737:chemistry* / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008274:Magnesium; D056004:Molecular Dynamics Simulation; D020559:Monomeric GTP-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D009154:Mutation; D010766:Phosphorylation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D000076106:SAM Domain and HD Domain-Containing Protein 1; D013379:Substrate Specificity; D013912:Threonine / Q000737:chemistry* / Q000378:metabolism
D003838:Deoxyadenine Nucleotides; D013912:Threonine; D018698:Glutamic Acid; D006160:Guanosine Triphosphate; D000076106:SAM Domain and HD Domain-Containing Protein 1; C484280:SAMHD1 protein, human; D020559:Monomeric GTP-Binding Proteins; D008274:Magnesium; C026600:2'-deoxyadenosine triphosphate
HIV-1 restriction factor; SAMHD1; all atom MD simulations; allostery