A formal methods approach to predicting new features of the eukaryotic vesicle traffic system

被引：5

作者：

Bhattacharyya, Arnab ^{[1
]}

Gupta, Ashutosh ^{[2
]}

Kuppusamy, Lakshmanan ^{[3
]}

Mani, Somya ^{[4
]}

Shukla, Ankit ^{[5
]}

Srivas, Mandayam ^{[6
]}

Thattai, Mukund ^{[7
]}

机构：

[1] Natl Univ Singapore, NUS Sch Comp, 13 Comp Dr, Singapore 117417, Singapore

[2] Indian Inst Technol, Mumbai 400076, Maharashtra, India

[3] VIT, Sch Comp Sci & Engn, Vellore 632014, Tamil Nadu, India

[4] IBS CSLM, Ulsan 44919, South Korea

[5] Johannes Kepler Univ Linz, A-4040 Linz, Austria

[6] Chennai Math Inst, Chennai 603103, Tamil Nadu, India

[7] NCBS TIFR, Simons Ctr Study Living Machines, Bengaluru 560065, India

来源：

ACTA INFORMATICA | 2021年 / 58卷 / 1-2期

基金：

奥地利科学基金会;

关键词：

GOLGI; MACHINERY; SNARES; GLYCOPROTEIN; PRINCIPLES; EVOLUTION; TRANSPORT; MEMBRANES; PROGRAM; COMPLEX;

D O I：

10.1007/s00236-019-00357-3

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

Vesicle traffic systems (VTSs) transport cargo among the intracellular compartments of eukaryotic cells. The compartments are viewed as nodes that are labeled by their chemical identity and the transport vesicles are similarly viewed as labeled edges between the nodes. Several interesting questions about VTSs translate to combinatorial search and synthesis problems. We present novel encodings for the problems based on Boolean satisfiability (SAT), satisfiability modulo theories and quantified Boolean formula of the properties over vesicle traffic systems. We have implemented the presented encodings in a tool that searches for the networks that satisfy properties related to transport consistency conditions using these solvers. In our numerical experiments, we show that our tool can search for networks of sizes that are relevant to real cellular systems. Our work illustrates the potential of novel biological applications of SAT solving technology.

引用

页码：57 / 93

页数：37

共 91 条

[61] Solving SAT and SAT modulo theories:: From an abstract Davis-Putnam-Logemann-Loveland procedure to DPLL(T) [J].

Nieuwenhuis, Robert ;

Oliveras, Albert ;

Tinelli, Cesare .

JOURNAL OF THE ACM, 2006, 53 (06) :937-977

[62] Cargo adaptors: structures illuminate mechanisms regulating vesicle biogenesis [J].

Paczkowski, Jon E. ;

Richardson, Brian C. ;

Fromme, J. Christopher .

TRENDS IN CELL BIOLOGY, 2015, 25 (07) :408-416

[63]

Paoletti N, 2014, LECT NOTES COMPUT SC, V8559, P343, DOI 10.1007/978-3-319-08867-9_23

[64] Structural aspects of Golgi function [J].

Polishchuk, RS ;

Mironov, AA .

CELLULAR AND MOLECULAR LIFE SCIENCES, 2004, 61 (02) :146-158

[65] Bidirectional traffic between the Golgi and the endosomes - machineries and regulation [J].

Progida, Cinzia ;

Bakke, Oddmund .

JOURNAL OF CELL SCIENCE, 2016, 129 (21) :3971-3982

[66] Evolutionary cell biology: functional insight from "endless forms most beautiful" [J].

Richardson, Elisabeth ;

Zerr, Kelly ;

Tsaousis, Anastasios ;

Dorrell, Richard G. ;

Dacks, Joel B. .

MOLECULAR BIOLOGY OF THE CELL, 2015, 26 (25) :4532-4538

[67] Rab conversion as a mechanism of progression from early to late endosomes [J].

Rink, J ;

Ghigo, E ;

Kalaidzidis, Y ;

Zerial, M .

CELL, 2005, 122 (05) :735-749

[68]

Robbins HE., 1939, AM MATH MONTHLY, DOI [10.2307/2303897, DOI 10.2307/2303897]

[69]

Rosenblueth DA, 2014, LECT N BIOINFORMAT, V8542, P235, DOI 10.1007/978-3-319-07953-0_19

[70] The machinery and principles of vesicle transport in the cell [J].

Rothman, JE .

NATURE MEDICINE, 2002, 8 (10) :1059-1062

← 1 2 3 4 5 6 7 8 9 10 →