A model for hydrophobic protrusions on peripheral membrane proteins
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With remarkable spatial and temporal specificities, peripheral membrane proteins bind to biological membranes. They do this without compromising solubility of the protein, and their binding sites are not easily distinguished. Prototypical peripheral membrane binding sites display a combination of patches of basic and hydrophobic amino acids that are also frequently present on other protein surfaces. The purpose of this contribution is to identify simple but essential components for membrane binding, through structural criteria that distinguish exposed hydrophobes at membrane binding sites from those that are frequently found on any protein surface. We formulate the concepts of protruding hydrophobes and co-insertability and have analysed more than 300 families of proteins that are classified as peripheral membrane binders. We find that this structural motif strongly discriminates the surfaces of membrane-binding and non-binding proteins. Our model constitutes a novel formulation of a structural pattern for membrane recognition and emphasizes the importance of subtle structural properties of hydrophobic membrane binding sites.
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15% of all disordered proteins bind lipid.
“it is perhaps not surprising that 15% of all disordered proteins bind lipid [288, 289].”
From Intrinsically disordered proteins play diverse roles in cell signaling (2022) · cites this paper as [289]
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R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952 · see citing works
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
van der Waals Volumes and Radii
Bondì, A. (1964) · The Journal of Physical Chemistry · doi:10.1021/j100785a001 · Cited by 19,375 · see citing works
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
Inference of macromolecular assemblies from crystalline state.
Krissinel, E., & Henrick, K. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.022 · Cited by 10,189 · see citing works
The quickhull algorithm for convex hulls
Barber, C. B., Dobkin, D., & Huhdanpaa, H. T. (1996) · ACM Transactions on Mathematical Software · doi:10.1145/235815.235821 · Cited by 5,364 · see citing works
OPM database and PPM web server: resources for positioning of proteins in membranes
Lomize, M. A., Pogozheva, I. D., Joo, H., Mosberg, H. I., & Lomize, A. L. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr703 · Cited by 2,126 · see citing works
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
Jakalian, A., Bush, B. L., Jack, D. B., & Bayly, C. I. (2000) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(20000130)21:2 · Cited by 1,681 · see citing works
Experimentally determined hydrophobicity scale for proteins at membrane interfaces
Wimley, W. C., & White, S. H. (1996) · Nature Structural & Molecular Biology · doi:10.1038/nsb1096-842 · Cited by 1,657 · see citing works
Membrane recognition by phospholipid-binding domains
Lemmon, M. A. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2328 · Cited by 1,455 · see citing works
Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., & Scharf, M. E. (1995) · Journal of Computational Chemistry · doi:10.1002/jcc.540160303 · Cited by 1,060 · see citing works
A series of PDB related databases for everyday needs
Joosten, R., Beek, T. T. T., Krieger, E., Hekkelman, M., Hooft, R., Schneider, R., Sander, C., & Vriend, G. (2010) · Nucleic Acids Res. · doi:10.1093/nar/gkq1105 · Cited by 1,050 · see citing works
Curvature of clathrin-coated pits driven by epsin
Ford, M. G. J., Mills, I. G., Peter, B. J., Vallis, Y., Praefcke, G. J. K., Evans, P. R., & McMahon, H. T. (2002) · Nature · doi:10.1038/nature01020 · Cited by 1,019 · see citing works
Analysis and prediction of the different types of β-turn in proteins
Wilmot, C. M., & Thornton, J. M. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90103-9 · Cited by 981 · see citing works
Interior and surface of monomeric proteins
Miller, S., Janin, J., Lesk, A. M., & Chothia, C. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90038-6 · Cited by 952 · see citing works
A series of PDB-related databanks for everyday needs
Touw, W. G., Baakman, C. A. B., Black, J., Beek, T. A. H. T., Krieger, E., Joosten, R. P., & Vriend, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1028 · Cited by 936 · see citing works
Fox, N. K., Brenner, S. E., & Chandonia, J.-M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1240 · Cited by 762 · see citing works
Interfacial Catalysis: the Mechanism of Phospholipase A 2
Scott, D. L., White, S. P., Otwinowski, Z., Yuan, W., Gelb, M. H., & Sigler, P. B. (1990) · Science · doi:10.1126/science.2274785 · Cited by 709 · see citing works
Zhang, G., Kazanietz, M. G., Blumberg, P. M., & Hurley, J. H. (1995) · Cell · doi:10.1016/0092-8674(95)90011-x · Cited by 653 · see citing works
Membrane-Protein Interactions in Cell Signaling and Membrane Trafficking
Cho, W., & Stahelin, R. V. (2005) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.33.110502.133337 · Cited by 615 · see citing works
Itoh, T., Erdmann, K. S., Roux, A., Habermann, B. H., Werner, H. B., & Camilli, P. V. D. (2005) · Developmental Cell · doi:10.1016/j.devcel.2005.11.005 · Cited by 585 · see citing works
Protein structure and function
(2004) · Choice Reviews Online · doi:10.5860/choice.41-4680 · Cited by 557 · see citing works
Endosomal sorting and signalling: an emerging role for sorting nexins
Cullen, P. J. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2427 · Cited by 431 · see citing works
PDBe: Protein Data Bank in Europe
Velankar, S. S., Best, C., Beuth, B., Boutselakis, C. H., Cobley, N., Silva, A. W. S. D., Dimitropoulos, D., Golovin, A., Hirshberg, M., John, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp916 · Cited by 337 · see citing works
The Crystal Structure of the PX Domain from p40phox Bound to Phosphatidylinositol 3-Phosphate
Bravo, J., Karathanassis, D., Pacold, C. M., Pacold, M. E., Ellson, C. D., Anderson, K. E., Butler, P. J. G., Lavenir, I., Perišić, O., Hawkins, P. T., et al. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00372-0 · Cited by 284 · see citing works
Amphitropic proteins: regulation by reversible membrane interactions (Review)
Johnson, J. E., & Cornell, R. B. (1999) · Molecular Membrane Biology · doi:10.1080/096876899294544 · Cited by 266 · see citing works
Misra, S., & Hurley, J. H. (1999) · Cell · doi:10.1016/s0092-8674(00)80776-x · Cited by 259 · see citing works
Translation of the phosphoinositide code by PI effectors
Kutateladze, T. G. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.390 · Cited by 251 · see citing works
Effective energy function for proteins in lipid membranes
Lazaridis, T. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10410 · Cited by 251 · see citing works
Crystal Structure of a Calcium-Phospholipid Binding Domain from Cytosolic Phospholipase A2*
Perisic, O., Fong, S., Lynch, D. E., Bycroft, M., & Williams, R. L. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.3.1596 · Cited by 247 · see citing works
The role of electrostatics in protein–membrane interactions
Mulgrew-Nesbitt, A., Diraviyam, K., Wang, J., Singh, S. P., MURRAY, P., LI, Z., ROGERS, L., MIRKOVIC, N., & MURRAY, D. (2006) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2006.07.002 · Cited by 185 · see citing works
Voltage-sensor activation with a tarantula toxin as cargo
Phillips, L. R., Milescu, M., Li‐Smerin, Y., Mindell, J. A., Kim, J. I., & Swartz, K. J. (2005) · Nature · doi:10.1038/nature03873 · Cited by 176 · see citing works
Structural Mechanism of Endosome Docking by the FYVE Domain
Kutateladze, T. G., & Overduin, M. (2001) · Science · doi:10.1126/science.291.5509.1793 · Cited by 175 · see citing works
Stahelin, R. V., Long, F., Diraviyam, K., Bruzik, K. S., Murray, D., & Cho, W. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m201106200 · Cited by 175 · see citing works
Stahelin, R. V., Long, F., Peter, B. J., Murray, D., Camilli, P. V. D., McMahon, H. T., & Cho, W. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m302865200 · Cited by 167 · see citing works
Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200020k · Cited by 159 · see citing works
Stahelin, R. V., & Cho, W. (2001) · Biochemistry · doi:10.1021/bi0020325 · Cited by 154 · see citing works
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces
Jones, S., Marin, A., & Thornton, J. M. (2000) · Protein Engineering Design and Selection · doi:10.1093/protein/13.2.77 · Cited by 151 · see citing works
Membrane Binding Mechanisms of the PX Domains of NADPH Oxidase p40 and p47
Stahelin, R. V., Burian, A., Bruzik, K. S., Murray, D., & Cho, W. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m212579200 · Cited by 143 · see citing works
Membrane permeabilization, orientation, and antimicrobial mechanism of subtilosin A
Thennarasu, S., Lee, D.-K., Poon, A., Kawulka, K. E., Vederas, J. C., & Ramamoorthy, A. (2005) · Chemistry and Physics of Lipids · doi:10.1016/j.chemphyslip.2005.06.003 · Cited by 134 · see citing works
The role of hydrophobic interactions in positioning of peripheral proteins in membranes
Lomize, A. L., Pogozheva, I. D., Lomize, M. A., & Mosberg, H. I. (2007) · BMC Structural Biology · doi:10.1186/1472-6807-7-44 · Cited by 127 · see citing works
Conformation and mode of membrane interaction in cyclotides
Shenkarev, Z. O., Nadezhdin, K. D., Sobol, V. A., Sobol, A. G., Skjeldal, L., & Arseniev, A. S. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05282.x · Cited by 125 · see citing works
Membrane interactions of G proteins and other related proteins
Vögler, O., Barceló, J. M., Ribas, C., & Escribá, P. V. (2008) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2008.03.008 · Cited by 116 · see citing works
Gilbert, G. E., Kaufman, R. J., Arena, A. A., Miao, H. Z., & Pipe, S. W. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m104732200 · Cited by 112 · see citing works
Sekino‐Suzuki, N., Nakamura, M., Mitsui, K., & Ohno‐Iwashita, Y. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.00941.x · Cited by 111 · see citing works
Frazier, A. A., Roller, C. R., Havelka, J. J., Hinderliter, A. K., & Cafiso, D. S. (2002) · Biochemistry · doi:10.1021/bi0268145 · Cited by 107 · see citing works
Insights from the X-ray Crystal Structure of Coral 8R-Lipoxygenase
Oldham, M. L., BRASH, A. R., & Newcomer, M. E. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m506675200 · Cited by 105 · see citing works
Lin, Y., Nielsen, R. D., Murray, D., Hubbell, W. L., Mailer, C., Robinson, B. H., & Gelb, M. H. (1998) · Science · doi:10.1126/science.279.5358.1925 · Cited by 102 · see citing works
Anderluh, G., Razpotnik, A., Podlesek, Z., Maček, P., Separovic, F., & Norton, R. S. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.12.058 · Cited by 93 · see citing works
Kohout, S. C., Corbalán‐García, S., Gómez-Fernández, J. C., & Falke, J. J. (2003) · Biochemistry · doi:10.1021/bi026596f · Cited by 87 · see citing works
SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins
Park, M.-J., Sheng, R., Silkov, A., Jung, D.-J., Wang, Z., Xin, Y., Kim, H., Thiagarajan‐Rosenkranz, P., Song, S.-H., Yoon, Y., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.027 · Cited by 86 · see citing works
Cation−π Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C
Grauffel, C., Yang, B., He, T., Roberts, M. F., Gershenson, A., & Reuter, N. (2013) · Journal of the American Chemical Society · doi:10.1021/ja312656v · Cited by 84 · see citing works
Self-citationInvestigations into Calcium-dependent Membrane Association of 15-Lipoxygenase-1
Walther, M., Wiesner, R., & Kühn, H. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m309564200 · Cited by 83 · see citing works
Rufener, E., Frazier, A. A., Wieser, C. M., Hinderliter, A., & Cafiso, D. S. (2005) · Biochemistry · doi:10.1021/bi048370d · Cited by 79 · see citing works
Malmberg, N. J., Buskirk, D. R. V., & Falke, J. J. (2003) · Biochemistry · doi:10.1021/bi035119+ · Cited by 70 · see citing works
Characterization of the Membrane Binding Mode of the C2 Domain of PKCε
Corbalán‐García, S., Sánchez-Carrillo, S., Garcı́a-Garcı́a, J., & Gómez-Fernández, J. C. (2003) · Biochemistry · doi:10.1021/bi034850d · Cited by 66 · see citing works
Kim, S. W., Quinn-Allen, M. A., Camp, J. T., Macedo‐Ribeiro, S., Fuentes‐Prior, P., Bode, W., & Kane, W. H. (2000) · Biochemistry · doi:10.1021/bi992256r · Cited by 64 · see citing works
Agasøster, A. V., Halskau, Ø., Fuglebakk, E., Frøystein, N. Å., Muga, A., Holmsen, H., & Martı́nez, A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211466200 · Cited by 61 · see citing works
Self-citationJian, X., Tang, W., Zhai, P. C., Roy, N. S., Luo, R., Gruschus, J. M., Yohe, M. E., Chen, P.-W., Li, Y., Byrd, R. A., et al. (2015) · Structure · doi:10.1016/j.str.2015.08.008 · Cited by 60 · see citing works
Role of Tryptophan Residues in Interfacial Binding of Phosphatidylinositol-specific Phospholipase C
Feng, J. A., Wehbi, H., & Roberts, M. F. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200938200 · Cited by 55 · see citing works
Canaan, S., Nielsen, R. D., Ghomashchi, F., Robinson, B. H., & Gelb, M. H. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m203649200 · Cited by 52 · see citing works
Wang, Q. J., Fang, T.-W., Nacro, K., Márquez, V. E., Wang, S., & Blumberg, P. M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m010089200 · Cited by 51 · see citing works
Gamsjaeger, R., Johs, A., Gries, A., Gruber, H. J., Romanin, C., Prassl, R., & Hinterdorfer, P. (2005) · Biochemical Journal · doi:10.1042/bj20050156 · Cited by 50 · see citing works
Interaction of Monotopic Membrane Enzymes with a Lipid Bilayer: A Coarse-Grained MD Simulation Study
Balali-Mood, K., Bond, P. J., & Sansom, M. S. P. (2009) · Biochemistry · doi:10.1021/bi8017398 · Cited by 49 · see citing works
Campos, B., Mo, Y., Mealy, T. R., Li, C. W., Swairjo, M. A., Balch, C., Head, J. W., Retzinger, G. S., Dedman, J. R., & Seaton, B. A. (1998) · Biochemistry · doi:10.1021/bi973142n · Cited by 47 · see citing works
Positioning Membrane Proteins by Novel Protein Engineering and Biophysical Approaches
Tatulian, S. A., Qin, S., Pande, A. H., & He, X. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.06.080 · Cited by 43 · see citing works
Gerber, S. H., Rizo, J., & Südhof, T. (2002) · Diabetes · doi:10.2337/diabetes.51.2007.s12 · Cited by 42 · see citing works
Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci2000192 · Cited by 38 · see citing works
Phospholipase Cβ1 induces membrane tubulation and is involved in caveolae formation
Inaba, T., Kishimoto, T., Murate, M., Tajima, T., Sakai, S., Abe, M., Makino, A., Tomishige, N., Ishitsuka, R., Ikeda, Y., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603513113 · Cited by 32 · see citing works
Are protein-protein interfaces special regions on a protein’s surface?
Tonddast-Navaei, S., & Skolnick, J. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4937428 · Cited by 31 · see citing works
Goh, B. C., Wu, H., Rynkiewicz, M. J., Schulten, K. J., Seaton, B. A., & McCormack, F. X. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00048 · Cited by 29 · see citing works
Chen, X., Wolfgang, D. E., & Sampson, N. S. (2000) · Biochemistry · doi:10.1021/bi001407j · Cited by 26 · see citing works
Feng, J. A., Bradley, W. D., & Roberts, M. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m301207200 · Cited by 23 · see citing works
Yang, B., Pu, M., Khan, H. M., Friedman, L. J., Reuter, N., Roberts, M. F., & Gershenson, A. (2014) · Journal of the American Chemical Society · doi:10.1021/ja508631n · Cited by 22 · see citing works
Self-citationIsas, J. M., Langen, R., Hubbell, W. L., & Haigler, H. T. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402568200 · Cited by 18 · see citing works
Hedin, E. M. K., Høyrup, P., Patkar, S. A., Vind, J., Svendsen, A., Fransson, L., & Hult, K. (2002) · Biochemistry · doi:10.1021/bi020158r · Cited by 16 · see citing works
Mathias, J. D., Ran, Y., Carter, J. D., & Fanucci, G. E. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2009.05.058 · Cited by 12 · see citing works
Changes in Ca2+ Affinity upon Activation of Agkistrodon piscivorus piscivorus Phospholipase A2
Lathrop, B. K., Gadd, M. E., Biltonen, R. L., & Rule, G. S. (2001) · Biochemistry · doi:10.1021/bi001901n · Cited by 8 · see citing works
Flagged first, then by citations
1 of the 80 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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Bondos, S. E., Dunker, A. K., & Uversky, V. N. (2022) · Cell Communication and Signaling · doi:10.1186/s12964-022-00821-7 · Cited by 222 · see citing works
Defining the subcellular distribution and metabolic channeling of phosphatidylinositol
Pemberton, J. G., Kim, Y. J., Humpolíčková, J., Eisenreichová, A., Sengupta, N., Tóth, D. J., Bouřa, E., & Balla, T. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201906130 · Cited by 96 · see citing works
Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling?
Cornish, J., Chamberlain, S. G., Owen, D., & Mott, H. R. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200467 · Cited by 69 · see citing works
Cookis, T., & Mattos, C. (2021) · Biomolecules · doi:10.3390/biom11070996 · Cited by 62 · see citing works
The energetics of protein–lipid interactions as viewed by molecular simulations
Corey, R. A., Stansfeld, P. J., & Sansom, M. S. P. (2019) · Biochemical Society Transactions · doi:10.1042/bst20190149 · Cited by 59 · see citing works
(2022) · doi:10.1177/25152564221134328 · Cited by 53 · see citing works
Larsen, A. H., John, L., Sansom, M. S. P., & Corey, R. A. (2022) · Bioscience Reports · doi:10.1042/bsr20211406 · Cited by 44 · see citing works
Waheed, Q., Khan, H. M., He, T., Roberts, M. F., Gershenson, A., & Reuter, N. (2019) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.9b01639 · Cited by 42 · see citing works
Self-citationA Perspective on the Prospective Use of AI in Protein Structure Prediction
Versini, R., Sritharan, S., Fas, B. A., Tubiana, T., Aimeur, S., Henri, J., Erard, M., Nüße, O., Andréani, J., Baaden, M., et al. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01361 · Cited by 33 · see citing works
Chatzigoulas, A., & Cournia, Z. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbab518 · Cited by 32 · see citing works
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Tubiana, T., Sillitoe, I., Orengo, C., & Reuter, N. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010346 · Cited by 28 · see citing works
Self-citationTatulian, S. A. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d4cp01136h · Cited by 24 · see citing works
Chatzigoulas, A., & Cournia, Z. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac680 · Cited by 19 · see citing works
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Koukos, P. I., Dehghani‐Ghahnaviyeh, S., Velez‐Vega, C., Manchester, J. I., Tieleman, D. P., Duca, J. S., Souza, P. C. T., & Cournia, Z. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00604 · Cited by 16 · see citing works
Ren, C., Zheng, Y., Liu, C., Mencius, J., Wu, Z., & Quan, S. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167405 · Cited by 14 · see citing works
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Agrawal, N., Skelton, A. A., & Parisini, E. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.04.013 · Cited by 8 · see citing works
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Seitter, H., Obkircher, J., Grabher, P., Hartl, J., Zanetti, L., Lux, U. T., Fotakis, G., Fernández‐Quintero, M. L., Kaserer, T., & Koschak, A. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.102972 · Cited by 2 · see citing works
Structure of AQEE-30 of VGF Neuropeptide in Membrane-Mimicking Environments
Park, O., Bang, J. K., Cheong, C., & Jeon, Y. H. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232213953 · Cited by 2 · see citing works
Poskin, L., Bâlon, H., Leyder, T., Michaux, C., & Mignon, J. (2026) · Critical Insights in Biophysics · doi:10.1080/29932203.2026.2638665
- Authors
- Fuglebakk, E., & Reuter, N.
- Affiliations
- University of Bergen (NO)
- Corresponding author
- Fuglebakk, Edvin
- Reuter, Nathalie
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-07-26
- Volume
- 14
- Issue
- 7
- Pages
- e1006325
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC6080788
- OpenAlex
- W2884293098
- Cited by
- 29
- References
- 80
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 1 · 2023: 6 · 2022: 9 · 2021: 5 · 2020: 1 · 2019: 3
- FWCI
- 0.80
- Type
- journal article
- Language
- en
- Update notices
- new_version (2018-08-07)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Norges Forskningsråd (214167, 251247)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- peripheral membrane proteins, membrane binding sites, membrane recognition, protein surface structure, hydrophobic amino acids, protein families, structural motifs
- MeSH terms
- Amino Acids, Binding Sites, Membrane Proteins, Models, Biological, Protein Binding, Hydrophobic and Hydrophilic Interactions, Datasets as Topic
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