Abraham M, Alekseenko A, Bergh C, Blau C, Briand E, Doijade M et al (2023) GROMACS 2023.1. Source code. https://doi.org/10.5281/zenodo.7852175

Ansah TA, Molla A, Katz S (1984) Ca2+-ATPase activity in pancreatic acinar plasma membranes. Regulation by calmodulin and acidic phospholipids. J Biol Chem 259:13442–13450. https://doi.org/10.1016/S0021-9258(18)90714-3

Article  CAS  PubMed  Google Scholar 

Baier CJ, Fantini J, Barrantes FJ (2011) Disclosure of cholesterol recognition motifs in transmembrane domains of the human nicotinic acetylcholine receptor. Sci Rep 1:69. https://doi.org/10.1038/srep00069

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Barrantes FJ (2013) How cholesterol interacts with membrane proteins: an exploration of cholesterol-binding sites including CRAC, CARC, and tilted domains. Front Physiol 4:31. https://doi.org/10.3389/fphys.2013.00031

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bhardwaj V, Purohit R (2020a) Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway. J Biomol Struct Dyn 38:1963–1974. https://doi.org/10.1080/07391102.2019.1621210

Article  CAS  PubMed  Google Scholar 

Bhardwaj VK, Purohit R (2020b) A new insight into protein-protein interactions and the effect of conformational alterations in PCNA. Int J Biol Macromol 148:999–1009. https://doi.org/10.1016/j.ijbiomac.2020.01.212

Article  CAS  PubMed  Google Scholar 

Bravo-Martínez J, Delgado-Coello B, Garcia DE, Mas-Oliva J (2011) Analysis of plasma membrane Ca2+-ATPase genes expression during epileptogenesis employing single hippocampal CA1 neurones. Exp Biol Med 236:409–417. https://doi.org/10.1258/ebm.2011.010342

Article  CAS  Google Scholar 

Briones-Orta MA, Delgado-Coello B, Gutiérrez-Vidal R, Sosa-Garrocho M, Macías-Silva M, Mas-Oliva J (2021) Quantitative expression of osteopontin and key cancer markers in the hepatocarcinoma AS-30D model. Front Oncol 11:670292. https://doi.org/10.3389/fonc.2021.670292

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brodin P, Falchetto R, Vorherr T, Carafoli E (1992) Identification of two domains which mediate the binding of activating PL to the plasma membrane Ca2+ pump. Eur J Biochem 204: 939–946. https://doi.org/10.1111/j.1432-1033.1992.tb16715.x

Cannarozzo C, Merve FS, Girych M, Bojone C, Enkavi G, Róg T et al (2021) Cholesterol-recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: the case of TRKB. Eur J Neurosci 53:3311–3322. https://doi.org/10.1111/ejn.15218

Article  CAS  PubMed  Google Scholar 

Caride AJ, Elwess NL, Verma AK, Filoteo AG, Enyedi A, Bajzer Z, Penniston JT (1999) The rate of activation by calmodulin of isoform 4 of the plasma membrane ca (2+) pump is slow and changed by alternative splicing. J Biol Chem 274:35227–35232. https://doi.org/10.1074/jbc.274.49.35227

Article  CAS  PubMed  Google Scholar 

Caride AJ, Filoteo AG, Penheiter AR, Pászty K, Enyedi A, Penniston JT (2001) Delayed activation of the plasma membrane calcium pump by a sudden increase in Ca2+: fast pumps reside in fast cells. Cell Calcium 30:49–57. https://doi.org/10.1054/ceca.2001.0212

Conrard L, Tyteca D (2019) Regulation of membrane calcium transport proteins by the surrounding lipid environment. 9:513. https://doi.org/10.3390/biom9100513

Daleke DL (2008) Regulation of phospholipid asymmetry in the erythrocyte membrane. Curr Opinion Hematol 15:191–195. https://doi.org/10.1097/MOH.0b013e3282f97af7

Davoudi S, Amjad-Iranagh S, Zaeifi Yamchi M (2015) Molecular dynamic simulation of Ca2+-ATPase interacting with lipid bilayer membrane. IET Nanobiotechnol 9:85–94. https://doi.org/10.1049/iet-nbt.2013.0073

Article  PubMed  Google Scholar 

Delgado-Coello B, Trejo R, Mas-Oliva J (2006) Is there a specific role for the plasma membrane Ca2+-ATPase in the hepatocyte? Mol Cell Biochem 285:1–15. https://doi.org/10.1007/s11010-005-9060-z

Delgado-Coello B, Montalvan-Sorrosa D, Cruz-Rangel A, Sosa-Garrocho M, Hernández-Téllez B, Macías-Silva M et al (2017) Label-free surface-enhanced Raman spectroscopy of lipid-rafts from hepatocyte plasma membranes. J Raman Spectrosc 48:659–667. https://doi.org/10.1002/jrs.5101

Article  ADS  CAS  Google Scholar 

Di Scala C, Fantini J (2017) Hybrid in silico/in vitro approaches for the identification of functional cholesterol-binding domains in membrane proteins. Methods Mol Biol 1583:7–19. https://doi.org/10.1007/978-1-4939-6875-6_2

Article  CAS  PubMed  Google Scholar 

Di Scala C, Baier CJ, Evans LS, Williamson PTF, Fantini J, Barrantes FJ (2017) Relevance of CARC and CRAC cholesterol-recognition motifs in the nicotinic acetylcholine receptor and other membrane-bound receptors. Curr Top Membr 80:3–23. https://doi.org/10.1016/bs.ctm.2017.05.001

Article  CAS  PubMed  Google Scholar 

Epand RM (2006) Cholesterol and the interaction of proteins with membrane domains. Prog Lipid Res 45:279–294. https://doi.org/10.1016/j.plipres.2006.02.001

Article  CAS  PubMed  Google Scholar 

Fantini J, Di Scala C, Evans LS, Williamson PT, Barrantes FJ (2016) A mirror code for protein-cholesterol interactions in the two leaflets of biological membranes. Sci Rep 6:21907. https://doi.org/10.1038/srep21907

Fatakia SN, Sarkar P, Chattopadhyay A (2020) Molecular evolution of a collage of cholesterol interaction motifs in transmembrane helix V of the serotonin1A receptor. Chem Phys Lipids 232:104955. https://doi.org/10.1016/j.chemphyslip.2020.104955

Article  CAS  PubMed  Google Scholar 

Fujimoto T (1993) Calcium pump of the plasma membrane is localized in caveolae. J Cell Biol 120:1147–1157. https://doi.org/10.1083/jcb.120.5.1147

Article  CAS  PubMed  Google Scholar 

Gál Z, Hegedüs C, Szakács G, Váradi A, Sarkadi B, Özvegy-Laczka C (2015) Mutations of the central tyrosines of putative cholesterol recognition amino acid consensus (CRAC) sequences modify folding, activity, and sterol-sensing of the human ABCG2 multidrug transporter. Biochim Biophys Acta 1848:477–487. https://doi.org/10.1016/j.bbamem.2014.11.006

Garcia A, Lev B, Hossain KK, Gorman A, Diaz D, Pham THN et al (2019) Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment. J Biol Chem 294:5956–5969. https://doi.org/10.1074/jbc.RA118.006223

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gong D, Chi X, Ren K, Huang G, Zhou G, Yan N et al (2018) Structure of the human plasma membrane Ca2+-ATPase PMCA1 in complex with its obligatory subunit neuroplastin. Nat Commun 9:3623. https://doi.org/10.1038/s41467-018-06075-7

Grouleff J, Irudayam SJ, Skeby KK, Schiott B (2015) The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations. Biochim Biophys Acta 1848:1783–1795. https://doi.org/10.1016/j.bbamem.2015.03.029

Article  CAS  PubMed  Google Scholar 

Hanson MA, Cherezov V, Roth CB, Griffith MT, Jaakola VP, Chien EY et al (2008) A specific cholesterol binding site is established by the 2.8 Å structure of the human ß2-adrenergic receptor in an alternate crystal form. Structure 16:897–905. https://doi.org/10.1016/j.str.2008.05.001

Huang J, Mackerel AD Jr (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34:2135–2145. https://doi.org/10.1002/jcc.23354

Article  CAS  PubMed  PubMed Central  Google Scholar 

Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38. https://doi.org/10.1016/0263-7855(96)00018-5

Article  CAS  PubMed  Google Scholar 

Jafurulla M, Chattopadhyay A (2017) Structural stringency of cholesterol for membrane protein function utilizing stereoisomers as novel tools: a review. Methods Mol Biol 1583:21–39. https://doi.org/10.1007/978-1-4939-6875-6_3

Article  CAS  PubMed  Google Scholar 

Jafurulla M, Tiwari S, Chattopadhyay A (2011) Identification of cholesterol recognition amino acid consensus (CRAC) motif in G-protein coupled receptors. Biochem Biophys Res Commun 404:569–573. https://doi.org/10.1016/j.bbrc.2010.12.031

Article  CAS  PubMed  Google Scholar 

Jiang L, Fernandes D, Mehta N, Bean JL, Michaelis ML, Zaidi A (2007) Partitioning of the plasma membrane Ca2+-ATPase into lipid rafts in primary neurons: effects of cholesterol depletion. J Neurochem 102:378–388. https://doi.org/10.1111/j.1471-4159.2007.04480.x

Jiang L, Bechtel MD, Galeva NA, Williams TD, Michaelis EK, Michaelis ML (2012) Decreases in plasma membrane Ca2+-ATPase in brain synaptic membrane rafts from aged rats. J Neurochem 123:689–699. https://doi.org/10.1111/j.1471-4159.2012.07918.x

Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: A Web-based graphical user interface for CHARMM. J Comput Chem 29:1859–1865. https://doi.org/10.1002/jcc.20945

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935. https://doi.org/10.1063/1.445869

Kessler F, Bennardini F, Bachs O, Serratosa J, James P, Gazzotti P, Penniston JT, Carafoli E (1990) Partial purification and characterization of the Ca2+-pumping ATPase of the liver plasma membrane. J Biol Chem 265:16012–16019. https://doi.org/10.1016/S0021-9258(18)55499-5

Krebs J (2022) Structure, function and regulation of the plasma membrane calcium pump in health and disease. Int J Mol Sci 23:1027. https://doi.org/10.3390/ijms2303102

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kumar GA, Sarkar P, Stepniewski TM, Jafurulla M, Singh SP, Selent J et al (2021) A molecular sensor for cholesterol in the human serotonin1A receptor. Sci Adv 7(30):eabh2922. https://www.science.org/doi/https://doi.org/10.1126/sciadv.abh2922

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Papadopoulos V (1998) Peripheral-type benzodiazepine receptor function in cholesterol transport. Identification of putative cholesterol recognition/interaction amino acid sequence and consensus pattern. Endocrinology 139:4991–4997. https://doi.org/10.1210/endo.139.12.6390

Article  CAS  PubMed  Google Scholar 

Lopreiato R, Giacomello M, Carafoli E (2014) The plasma membrane calcium pump: new ways to look at and old enzyme. J Biol Chem 289:10261–10268. https://doi.org/10.1074/jbc.O114.555565

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lotersztajn S, Pavoine C, Deterre P, Capeau J, Mallat A, LeNguyen D et al (1992) Role of G protein βγ subunits in the regulation of the plasma membrane Ca2+ pump. J Biol Chem 208: 2375–2379. https://doi.org/10.1016/S0021-9258(18)45889-9

Lushington GH, Zaidi A, Michaelis ML (2005) Theoretically predicted structures of plasma membrane Ca(2+)-ATPase and their susceptibilities to oxidation. J Mol Graph Model 24:175–185. https://doi.org/10.1016/j.jmgm.2005.07.003

Luz-Madrigal A, Asanov A, Camacho-Zarco AR, Sampieri A, Vaca L (2013) Cholesterol recognition amino acid consensus domain in GP64 fusion protein facilitates anchoring of baculovirus to mammalian cells. J Virol 87:11894–11907. https://doi.org/10.1128/JVI.01356-13

Mas-Oliva J, Delgado-Coello B (2007) Protein stability and the evolution of the cell membrane. Comp Biochem Physiol Part C Toxicol & Pharmacol 146:207–213. https://doi.org/10.1016/j.cbpc.2006.09.007

Mas-Oliva J, Santiago-García J (1990) Cholesterol effect on thermostability of the (Ca2+, Mg2+)-ATPase from cardiac muscle sarcolemma. Biochem Intl 21:233–241

CAS