Integrative Multiscale Simulations Uncover the Mechanistic Principles Governing COPII Mediated Vesicle Formation

Arkhipov A, Yin Y, Schulten K (2008) Four-scale description of membrane sculpting by BAR domains. Biophys J 95:2806–2821

Article  PubMed  PubMed Central  CAS  Google Scholar 

Arkhipov A, Yin Y, Schulten K (2009) Membrane-bending mechanism of amphiphysin N-BAR domains. Biophys J 97:2727–2735

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G (2019) Nat Commun 10:2370

Article  PubMed  PubMed Central  Google Scholar 

Bi X, Corpina RA, Goldberg J (2002) Nature 419:271–277

Article  PubMed  CAS  Google Scholar 

Bielli A, Haney CJ, Gabreski G, Watkins SC, Bannykh SI, Aridor M (2005) Regulation of Sar1 NH2 terminus by GTP binding and hydrolysis promotes membrane deformation to control COPII vesicle fission. J Cell Biol 171:919–924

Article  PubMed  PubMed Central  CAS  Google Scholar 

Blood PD, Voth GA (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 15068–15072

Blood PD, Swenson RD, Voth GA (2008) Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations. Biophys J 95:1866–1876

Article  PubMed  PubMed Central  CAS  Google Scholar 

Boerner TJ, Deems S, Furlani TR, Knuth SL, Towns J (2023) In Practice and Experience in Advanced Research Computing (PEARC ’23)

Flood JR, Mendina CA, Audhya A (2025) Organizing principles underlying COPII-mediated transport. Curr Opin Cell Biol 94:102492

Article  PubMed  CAS  Google Scholar 

Fonin AV, Antifeeva IA, Kuznetsova IM, Turoverov KK, Zaslavsky BY, Kulkarni P, Uversky VN (2022) <article-title update="added">Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates. Essays Biochem 66:831–847

Article  PubMed  CAS  Google Scholar 

Gallo R, Rai AK, McIntyre AB, Meyer K, Pelkmans L (2023) Dev Cell 58:1880–1897

Article  PubMed  CAS  Google Scholar 

Hanna MG, Mela I, Wang L, Henderson RM, Chapman ER, Edwardson JM, Audhya A (2016) Sar1 GTPase activity is regulated by membrane curvature. J Biol Chem 291:1014–1027

Article  PubMed  CAS  Google Scholar 

Hariri H, Bhattacharya N, Johnson K, Noble AJ, Stagg SM (2014) Insights into the mechanisms of membrane curvature and vesicle scission by the small GTPase Sar1 in the early secretory pathway. J Mol Biol 426:3811–3826

Article  PubMed  PubMed Central  CAS  Google Scholar 

Helfrich W (1973) Elastic properties of lipid bilayers: theory and possible experiments. Z Naturforsch C 28:693–703

Article  PubMed  CAS  Google Scholar 

Hutchings J, Stancheva V, Miller EA, Zanetti G (2018) Nat Commun 9:1–8

Article  CAS  Google Scholar 

Kozlov MM, Taraska JW (2023) Nat Rev Mol Cell Biol 24:63–78

Article  PubMed  CAS  Google Scholar 

Kuehn MJ, Herrmann JM, Schekman R (1998) Nature 391:187–190

Article  PubMed  CAS  Google Scholar 

Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T (2001) Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Proc Natl Acad Sci U S A 98:10704–10709

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lee MC, Orci L, Hamamoto S, Futai E, Ravazzola M, Schekman R (2005) Sar1p N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle. Cell 122:605–617

Article  PubMed  CAS  Google Scholar 

Long KR, Yamamoto Y, Baker AL, Watkins SC, Coyne CB, Conway JF, Aridor M (2010) Sar1 assembly regulates membrane constriction and ER export. J Cell Biol 190:115–128

Article  PubMed  PubMed Central  CAS  Google Scholar 

Maeda M, Katada T, Saito K (2017) TANGO1 recruits Sec16 to coordinately organize ER exit sites for efficient secretion. J Cell Biol 216:1731–1743

Article  PubMed  PubMed Central  CAS  Google Scholar 

Malshikare H, Prakash S, Sengupta D (2023) Soft Matter 19:4021–4028

Article  PubMed  CAS  Google Scholar 

Mandal T, Lough W, Spagnolie SE, Audhya A, Cui Q (2020) Molecular simulation of mechanical properties and membrane activities of the ESCRT-III complexes. Biophys J 118:1333–1343

Article  PubMed  PubMed Central  CAS  Google Scholar 

Matsuoka K, Orci L, Amherdt M, Bednarek SY, Hamamoto S, Schek- man R, Yeung T (1998) Cell 93:263–275

Article  PubMed  CAS  Google Scholar 

Mondal S, Cui Q (2022) Coacervation of poly-electrolytes in the presence of lipid bilayers: mutual alteration of structure and morphology. Chem Sci 13:7933–7946

Article  PubMed  PubMed Central  CAS  Google Scholar 

Nakano A, Brada D, Schekman R (1988) A membrane glycoprotein, Sec12p, required for protein transport from the endoplasmic reticulum to the Golgi apparatus in yeast. J Cell Biol 107:851–863

Article  PubMed  CAS  Google Scholar 

Ohkubo YZ, Pogorelov TV, Arcario MJ, Christensen GA (2012) Tajkhor- shid, E. Biophys J 102:2130–2139

Article  PubMed  PubMed Central  CAS  Google Scholar 

Paul S, Ainavarapu SRK, Venkatramani R (2020) <article-title update="added">Variance of atomic coordinates as a dynamical metric to distinguish proteins and protein–protein interactions in molecular dynamics simulations. J Phys Chem B 124:4247–4262

Article  PubMed  CAS  Google Scholar 

Paul S, Audhya A, Cui Q (2023) <article-title update="added">Molecular mechanism of GTP binding- and dimerization-induced enhancement of Sar1-mediated membrane remodeling. Proc Natl Acad Sci U S A 120:e2212513120

Article  PubMed  PubMed Central  CAS  Google Scholar 

Paul S, Audhya A, Cui Q (2024) PNAS Nexus 3:pgae305

Article  PubMed  PubMed Central  CAS  Google Scholar 

Paul S, Mondal S, Piskulich ZA, Mandal T, Cui Q (2025) Membrane shape and biological function. CRC, pp 107–132

Prakash S, Krishna A, Sengupta D (2021) Faraday Discuss 232:218–235

Article  PubMed  Google Scholar 

Pyle E, Miller EA, Zanetti G (2025) Nat Struct Mol Biol 32:513–519

Article  PubMed  CAS  Google Scholar 

Ramakrishnan N, Sunil Kumar P, Ipsen JH (2010) Monte Carlo simulations of fluid vesicles with in-plane orientational ordering. Phys Rev E 81:041922

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