A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility

References

• Blasko I, Beer R, Bigl M, et al. Experimental traumatic brain injury in rats stimulates the expression, production and activity of Alzheimer’s disease beta-secretase (BACE-1). J Neural Transm 2004;111:523–36
   PubMed Web of Science ®Google Scholar
• Cruts M, Dermaut B, Rademakers R, et al. Amyloid beta secretase gene (BACE) is neither mutated in nor associated with early-onset Alzheimer’s disease. Neurosci Lett 2001;313:105–7
   PubMed Web of Science ®Google Scholar
• Miri R, Firuzi O, Razzaghi-Asl N, et al. Inhibitors of Alzheimer’s BACE-1 with 3,5-bis-N-(aryl/heteroaryl) carbamoyl-4-aryl-1,4-dihydropyridine structure. Arch Pharm Res 2015;38:456–69
   PubMed Web of Science ®Google Scholar
• Videira R, Castanheira P, Graos M, et al. A necrodane monoterpenoid from Lavandula luisieri essential oil as a cell-permeable inhibitor of BACE-1, the beta-secretase in Alzheimer’s disease. Flav Frag J 2013;28:380–8
   Web of Science ®Google Scholar
• Lopez-Font I, Cuchillo-Ibanez I, Sogorb-Esteve A, et al. Transmembrane Amyloid-related proteins in CSF as potential biomarkers for Alzheimer’s disease. Front Neurol 2015;6:125
   PubMed Web of Science ®Google Scholar
• Klinger SC, Siupka P, Nielsen MS. Retromer-mediated trafficking of transmembrane receptors and transporters. Membranes 2015;5:288–306
   PubMed Web of Science ®Google Scholar
• Chen M. The maze of APP processing in Alzheimer’s disease: where did we go wrong in reasoning?. Front Cell Neurosci 2015;9:186
   PubMed Web of Science ®Google Scholar
• Cai Z, Chen G, He W, et al. Activation of mTOR: a culprit of Alzheimer’s disease?. Neuropsychiatr Dis Treat 2015;11:1015–30
   PubMed Web of Science ®Google Scholar
• Vassar R, Kuhn PH, Haass C, et al. Function, therapeutic potential and cell biology of BACE proteases: current status and future prospects. J Neurochem 2014;130:4–28
   PubMed Web of Science ®Google Scholar
• Oehlrich D, Prokopcova H, Gijsen HJ. The evolution of amidine-based brain penetrant BACE1 inhibitors. Bioorg Med Chem Lett 2014;24:2033–45
   PubMed Web of Science ®Google Scholar
• Butini S, Brogi S, Novellino E, et al. The structural evolution of beta-secretase inhibitors: a focus on the development of small-molecule inhibitors. Curr Top Med Chem 2013;13:1787–807
   PubMed Web of Science ®Google Scholar
• Kim YT, Downs D, Wu SL, et al. Enzymic properties of recombinant BACE2. Eur J Biochem 2002;269:5668–77
   PubMedGoogle Scholar
• Lahiri DK, Maloney B, Ge YW. Functional domains of the BACE1 and BACE2 promoters and mechanisms of transcriptional suppression of the BACE2 promoter in normal neuronal cells. J Mol Neurosci 2006;29:65–80
   PubMed Web of Science ®Google Scholar
• Liu X, Wang Z, Wu Y, et al. BACE2 degradation mediated by the macroautophagy-lysosome pathway. Eur J Neurosci 2013;37:1970–7
   PubMed Web of Science ®Google Scholar
• Ostermann N, Eder J, Eidhoff U, et al. Crystal structure of human BACE2 in complex with a hydroxyethylamine transition-state inhibitor. J Mol Biol 2006;355:249–61
   PubMed Web of Science ®Google Scholar
• Sun XL, Wang YX, Qing H, et al. Distinct transcriptional regulation and function of the human BACE2 and BACE1 genes. FASEB J 2005;19:739–49
   PubMed Web of Science ®Google Scholar
• Southan C. BACE2 as a new diabetes target: a patent review (2010–2012). Expert Opin Ther Pat 2013;23:649–63
   PubMed Web of Science ®Google Scholar
• Prox J, Rittger A, Saftig P. Physiological functions of the amyloid precursor protein secretases ADAM10, BACE1, and presenilin. Exp Brain Res 2012;217:331–41
   PubMed Web of Science ®Google Scholar
• Zhu ZW, Schuster DI, Tuckerman ME. Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease. Biochemistry 2003;42:1326–33
   PubMed Web of Science ®Google Scholar
• Xu Y, Li MJ, Greenblatt H, et al. Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations. Acta Crystallogr Sect D Biol Crystallogr 2012;68:13–25
   PubMed Web of Science ®Google Scholar
• Hong L, Tang J. Flap position of free memapsin 2 (beta-secretase), a model for flap opening in aspartic protease catalysis. Biochemistry 2004;43:4689–95
   PubMed Web of Science ®Google Scholar
• Heaslet H, Rosenfeld R, Giffin M, et al. Conformational flexibility in the flap domains of ligand-free HIV protease. Acta Crystallogr D Biol Crystallogr 2007;63:866–75
   PubMed Web of Science ®Google Scholar
• Cai Y, Kurt Yilmaz N, Myint W, et al. Differential flap dynamics in wild-type and a drug resistant variant of HIV-1 protease revealed by molecular dynamics and NMR relaxation. J Chem Theor Comput 2012;8:3452–62
   PubMed Web of Science ®Google Scholar
• Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci USA 2006;103:915–20
   PubMed Web of Science ®Google Scholar
• Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007;157:606–15
   PubMed Web of Science ®Google Scholar
• Kovalskyy D, Dubyna V, Mark AE, Kornelyuk A. A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: the role of Na + ions in stabilizing the active site. Proteins 2005;58:450–8
   PubMed Web of Science ®Google Scholar
• Karubiu W, Bhakat S, McGillewie L, Soliman MES. Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics. Mol Biosyst 2015;11:1061–6
   PubMed Web of Science ®Google Scholar
• Stsiapanava A, Olsson U, Wan M, et al. Binding of Pro-Gly-Pro at the active site of leukotriene A(4) hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor. Proc Natl Acad Sci USA 2014;111:4227–32
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605–12
   PubMed Web of Science ®Google Scholar
• Gotz AW, Williamson MJ, Xu D, et al. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput 2012;8:1542–55
   PubMed Web of Science ®Google Scholar
• Case DA, Cheatham TE III, Simmerling CL, et al. AMBER 12. San Francisco: University of California; 2012
   Google Scholar
• Swope WC, Pitera JW, Suits F, et al. Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and beta-hairpin peptide. J Phys Chem B 2004;108:6582–94
   Web of Science ®Google Scholar
• Wang JM, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem 2004;25:1157–74
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen K, Piana S, Palmo K, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 2010;78:1950–8
   PubMed Web of Science ®Google Scholar
• Stote RH, Karplus M. Zinc-binding in proteins and solution – a simple but accurate nonbonded representation. Proteins 1995;23:12–31
   PubMed Web of Science ®Google Scholar
• Harvey MJ, De Fabritiis G. An Implementation of the smooth particle mesh Ewald method on GPU hardware. J Chem Theory Comput 2009;5:2371–7
   PubMed Web of Science ®Google Scholar
• Le Grand S, Goetz AW, Walker RC. SPFP: speed without compromise – a mixed precision model for GPU accelerated molecular dynamics simulations. Comput Phys Commun 2013;184:374–80
   Web of Science ®Google Scholar
• Roe DR, Cheatham TE. III PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 2013;9:3084–95
   PubMed Web of Science ®Google Scholar
• Cocco S, Monasson R, Weigt M. From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol 2013;9:e1003176
   Google Scholar
• Mirsafian H, Mat Ripen A, Merican AF, Mohamad SB. Amino acid sequence and structural comparison of BACE1 and BACE2 using evolutionary trace method. Sci World J 2014;2014:6
   Google Scholar
• Gorfe AA, Caflisch A. Functional plasticity in the substrate binding site of beta-secretase. Structure (London, England: 1993) 2005;13:1487–98
   PubMed Web of Science ®Google Scholar
• Jolliffe, IT. Principal component analysis. New York: Springer; 2002
   Google Scholar
• Patel S, Vuillard L, Cleasby A, et al. Apo and inhibitor complex structures of BACE (β-secretase). J Mol Biol 2004;343:407–16
   PubMed Web of Science ®Google Scholar
• Kumalo, HM, Bhakat, S, Soliman, ME. Investigation of flap flexibility of beta-secretase using molecular dynamic simulations. J Biomol Struct Dyn 2015;1–12
   PubMed Web of Science ®Google Scholar