F the memory stochastic simulation algorithm (memory-SSA); the theory of the memory Gracillin chemical information chemical master equation and memory stochastic differential equations; assumptions, chemical reactions and rate constants of a stochastic model with memory reactions for 22948146 describing theexpression of a single gene and for the stochastic model of the p53-MDM2 regulatory network. (PDF)Author ContributionsConceived and designed the experiments: TT. Performed the experiments: TT. Analyzed the data: TT. Contributed reagents/materials/analysis tools: TT. Wrote the paper: TT.
Mucolipidosis type IV (MLIV) is a neurodegenerative lysosomal storage disorder that is characterized by severe psychomotor retardation, achlorhydria, and ophthalmological abnormalities that lead to blindness. Most tissues in MLIV patients show lysosomal defects, yet death primarily occurs in neurons [1,2]. MLIV is caused by mutations in the MCOLN1 gene, which encodes a transient receptor potential ion channel protein called mucolipin-1/TRPML1 [3,4,5]. The TRPML1 channel is permeable to cations and localizes primarily to late endosomes/ lysosomes [6,7,8,9,10,11,12]. Over 20 different mutations in MCOLN1 have been identified in MLIV patients, although two founder mutations account for ,95 of all MLIV alleles and show a heterozygote frequency of 1:100 in the Ashkenazi Jewish population [13,14]. There are two other homologues of TRPML1, TRPML2 and TRPML3, and the three TRPMLs homo- and hetero-multimerize [15,16]. Studies on MLIV cells have identified many lysosomalassociated defects, including defects in transport to lysosomes [17,18,19,20], in lysosomal degradation leading to 
accumulation of material [21,22], in lysosomal exocytosis [23], in lipid transport from endosomes to the Golgi apparatus [11,19,24], in metal homeostasis [7,8], in macroautophagy [25,26], in chaperonemediated autophagy [27], and in mitochondrial function [28]. Yet the question still remains: which transport steps that are defective in MLIV cells are normally directly regulated by TRPML1? Forexample, does TRPML1 directly regulate lipid transport from endosomes to the Golgi apparatus, or is this defect in the absence of TRPML1 indirect, perhaps due to altered late endosomes/ lysosomes? Furthermore, how does TRPML1 regulate the different transport steps? One approach to begin to answer questions about the biochemical functions of TRPML1 is to identify proteins that directly associate with TRPML1 and/or are found in a TRPML1containing complex. 15755315 The molecular identities of these interactors may immediately suggest testable mechanisms. Furthermore, interfering with the functions of these interactors may implicate specific transport steps that they regulate in association with TRPML1. Previous studies identified three classes of proteins that physically associate with TRPML1. First, Alix/Apoptosis-Linked AN-3199 Gene-2 (ALG-2) is a penta-EF hand protein that binds the amino terminus of TRPML1 [20]. Second, Lysosomal-Associated Protein Transmembrane (LAPTM)-4a, LAPTM-4b, and LAPTM-5 associate with TRPML1 on endosomes/lysosomes [29]. Third, TRPML1 is also thought to associate 
with the chaperones Hsc70 and Hsp40 and other members of the Chaperone-Mediated Autophagy complex. While the physiological significance of the first two class of interactions has yet to be elucidated, TRPML1 is thought to regulate Chaperone-Mediated Autophagy through its interactions with the third class of proteins [27]. In this study, we systematically screen for add.F the memory stochastic simulation algorithm (memory-SSA); the theory of the memory chemical master equation and memory stochastic differential equations; assumptions, chemical reactions and rate constants of a stochastic model with memory reactions for 22948146 describing theexpression of a single gene and for the stochastic model of the p53-MDM2 regulatory network. (PDF)Author ContributionsConceived and designed the experiments: TT. Performed the experiments: TT. Analyzed the data: TT. Contributed reagents/materials/analysis tools: TT. Wrote the paper: TT.
Mucolipidosis type IV (MLIV) is a neurodegenerative lysosomal storage disorder that is characterized by severe psychomotor retardation, achlorhydria, and ophthalmological abnormalities that lead to blindness. Most tissues in MLIV patients show lysosomal defects, yet death primarily occurs in neurons [1,2]. MLIV is caused by mutations in the MCOLN1 gene, which encodes a transient receptor potential ion channel protein called mucolipin-1/TRPML1 [3,4,5]. The TRPML1 channel is permeable to cations and localizes primarily to late endosomes/ lysosomes [6,7,8,9,10,11,12]. Over 20 different mutations in MCOLN1 have been identified in MLIV patients, although two founder mutations account for ,95 of all MLIV alleles and show a heterozygote frequency of 1:100 in the Ashkenazi Jewish population [13,14]. There are two other homologues of TRPML1, TRPML2 and TRPML3, and the three TRPMLs homo- and hetero-multimerize [15,16]. Studies on MLIV cells have identified many lysosomalassociated defects, including defects in transport to lysosomes [17,18,19,20], in lysosomal degradation leading to accumulation of material [21,22], in lysosomal exocytosis [23], in lipid transport from endosomes to the Golgi apparatus [11,19,24], in metal homeostasis [7,8], in macroautophagy [25,26], in chaperonemediated autophagy [27], and in mitochondrial function [28]. Yet the question still remains: which transport steps that are defective in MLIV cells are normally directly regulated by TRPML1? Forexample, does TRPML1 directly regulate lipid transport from endosomes to the Golgi apparatus, or is this defect in the absence of TRPML1 indirect, perhaps due to altered late endosomes/ lysosomes? Furthermore, how does TRPML1 regulate the different transport steps? One approach to begin to answer questions about the biochemical functions of TRPML1 is to identify proteins that directly associate with TRPML1 and/or are found in a TRPML1containing complex. 15755315 The molecular identities of these interactors may immediately suggest testable mechanisms. Furthermore, interfering with the functions of these interactors may implicate specific transport steps that they regulate in association with TRPML1. Previous studies identified three classes of proteins that physically associate with TRPML1. First, Alix/Apoptosis-Linked Gene-2 (ALG-2) is a penta-EF hand protein that binds the amino terminus of TRPML1 [20]. Second, Lysosomal-Associated Protein Transmembrane (LAPTM)-4a, LAPTM-4b, and LAPTM-5 associate with TRPML1 on endosomes/lysosomes [29]. Third, TRPML1 is also thought to associate with the chaperones Hsc70 and Hsp40 and other members of the Chaperone-Mediated Autophagy complex. While the physiological significance of the first two class of interactions has yet to be elucidated, TRPML1 is thought to regulate Chaperone-Mediated Autophagy through its interactions with the third class of proteins [27]. In this study, we systematically screen for add.
