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For: Mravic M, Thomaston JL, Tucker M, Solomon PE, Liu L, DeGrado WF. Packing of apolar side chains enables accurate design of highly stable membrane proteins. Science 2019;363:1418-1423. [PMID: 30923216 DOI: 10.1126/science.aav7541] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Niitsu A, Thomson AR, Scott AJ, Sengel JT, Jung J, Mahendran KR, Sodeoka M, Bayley H, Sugita Y, Woolfson DN, Wallace MI. Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels. J Am Chem Soc 2025;147:11741-11753. [PMID: 40152328 DOI: 10.1021/jacs.4c13933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2025]
2
Chen KYM, Lai JK, Rudden LSP, Wang J, Russell AM, Conners K, Rutter ME, Condon B, Tung F, Kodandapani L, Chau B, Zhao X, Benach J, Baker K, Hembre EJ, Barth P. Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks. Nat Chem 2025;17:429-438. [PMID: 39849110 PMCID: PMC11882447 DOI: 10.1038/s41557-024-01719-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/11/2024] [Indexed: 01/25/2025]
3
Kurgan KW, Martin FJO, Dawson WM, Brunnock T, Orr-Ewing AJ, Woolfson DN. Exchange, promiscuity, and orthogonality in de novo designed coiled-coil peptide assemblies. Chem Sci 2025;16:1826-1836. [PMID: 39720134 PMCID: PMC11664599 DOI: 10.1039/d4sc06329e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 12/02/2024] [Indexed: 12/26/2024]  Open
4
Muhammednazaar S, Yao J, Necelis MR, Park YC, Shen Z, Bridges MD, Guo R, Swope N, Rhee MS, Kim M, Kim KH, Hubbell WL, Fleming KG, Columbus L, Kang SG, Hong H. Lipid bilayer strengthens the cooperative network of membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.30.542905. [PMID: 37398072 PMCID: PMC10312574 DOI: 10.1101/2023.05.30.542905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
5
Liu Y, Weidle C, Mihaljević L, Watson JL, Li Z, Yu LT, Majumder S, Borst AJ, Carr KD, Kibler RD, El-Din TMG, Catterall WA, Baker D. Bottom-up design of calcium channels from defined selectivity filter geometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.19.629320. [PMID: 39763961 PMCID: PMC11702685 DOI: 10.1101/2024.12.19.629320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2025]
6
Samanta R, Harmalkar A, Prathima P, Gray JJ. Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta. J Chem Theory Comput 2024;20:10740-10749. [PMID: 39574325 PMCID: PMC12025977 DOI: 10.1021/acs.jctc.4c00927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
7
Wang M, Ma A, Wang H, Lou X. Atomic molecular dynamics simulation advances of de novo-designed proteins. Q Rev Biophys 2024;57:e14. [PMID: 39635823 DOI: 10.1017/s0033583524000131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
8
Weber DK, Reddy UV, Robia SL, Veglia G. Pathological mutations in the phospholamban cytoplasmic region affect its topology and dynamics modulating the extent of SERCA inhibition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024;1866:184370. [PMID: 38986894 PMCID: PMC11457527 DOI: 10.1016/j.bbamem.2024.184370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
9
Hardy BJ, Curnow P. Computational design of de novo bioenergetic membrane proteins. Biochem Soc Trans 2024;52:1737-1745. [PMID: 38958574 PMCID: PMC11668274 DOI: 10.1042/bst20231347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
10
Deb R, Torres MDT, Boudný M, Koběrská M, Cappiello F, Popper M, Dvořáková Bendová K, Drabinová M, Hanáčková A, Jeannot K, Petřík M, Mangoni ML, Balíková Novotná G, Mráz M, de la Fuente-Nunez C, Vácha R. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. J Med Chem 2024;67:14040-14061. [PMID: 39116273 PMCID: PMC11345766 DOI: 10.1021/acs.jmedchem.4c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
11
Rathod N, Lemieux MJ, Chipot C, Roux B, Young HS. Probing the formation of a hetero-dimeric membrane transport complex with dual in vitro and in silico mutagenesis. Chem Sci 2024:d4sc02915a. [PMID: 39156929 PMCID: PMC11322925 DOI: 10.1039/d4sc02915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]  Open
12
Samanta R, Harmalkar A, Prathima P, Gray JJ. Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602802. [PMID: 39026849 PMCID: PMC11257521 DOI: 10.1101/2024.07.09.602802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
13
Yao J, Hong H. Steric trapping strategy for studying the folding of helical membrane proteins. Methods 2024;225:1-12. [PMID: 38428472 PMCID: PMC11107808 DOI: 10.1016/j.ymeth.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]  Open
14
Yang H, Zhou D, Zhou Z, Duan M, Yu H. Mechanistic Insight into the Mechanical Unfolding of the Integral Membrane Diacylglycerol Kinase. JACS AU 2024;4:1422-1435. [PMID: 38665647 PMCID: PMC11040704 DOI: 10.1021/jacsau.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/28/2024]
15
Chu AE, Lu T, Huang PS. Sparks of function by de novo protein design. Nat Biotechnol 2024;42:203-215. [PMID: 38361073 PMCID: PMC11366440 DOI: 10.1038/s41587-024-02133-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
16
Xu B, Chen Y, Xue W. Computational Protein Design - Where it goes? Curr Med Chem 2024;31:2841-2854. [PMID: 37272467 DOI: 10.2174/0929867330666230602143700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 06/06/2023]
17
Medeiros-Silva J, Dregni AJ, Somberg NH, Duan P, Hong M. Atomic structure of the open SARS-CoV-2 E viroporin. SCIENCE ADVANCES 2023;9:eadi9007. [PMID: 37831764 PMCID: PMC10575589 DOI: 10.1126/sciadv.adi9007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023]
18
Yu CP, Kumagai S, Tsutsumi M, Kurosawa T, Ishii H, Watanabe G, Hashizume D, Sugiura H, Tani Y, Ise T, Watanabe T, Sato H, Takeya J, Okamoto T. Asymmetrically Functionalized Electron-Deficient π-Conjugated System for Printed Single-Crystalline Organic Electronics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023;10:e2207440. [PMID: 37712117 PMCID: PMC10582418 DOI: 10.1002/advs.202207440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/22/2023] [Indexed: 09/16/2023]
19
Das A, K V, S SD, Mahendran KR. Synthetic α-Helical Nanopore Reactor for Chemical Sensing. JACS AU 2023;3:2467-2477. [PMID: 37772177 PMCID: PMC10523496 DOI: 10.1021/jacsau.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 09/30/2023]
20
Sučec I, Mammeri NE, Dregni AJ, Hong M. Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR. J Phys Chem B 2023;127:7518-7530. [PMID: 37606918 PMCID: PMC10893779 DOI: 10.1021/acs.jpcb.3c05295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
21
Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem 2023;15:1012-1021. [PMID: 37308712 PMCID: PMC10475958 DOI: 10.1038/s41557-023-01210-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 06/14/2023]
22
Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023;35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
23
Hederman AP, Ackerman ME. Leveraging deep learning to improve vaccine design. Trends Immunol 2023;44:333-344. [PMID: 37003949 PMCID: PMC10485910 DOI: 10.1016/j.it.2023.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/05/2023] [Accepted: 03/05/2023] [Indexed: 04/03/2023]
24
Smalinskaitė L, Hegde RS. The Biogenesis of Multipass Membrane Proteins. Cold Spring Harb Perspect Biol 2023;15:a041251. [PMID: 36096638 PMCID: PMC10071439 DOI: 10.1101/cshperspect.a041251] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
25
Menke FS, Wicher B, Maurizot V, Huc I. Homochiral versus Heterochiral Dimeric Helical Foldamer Bundles: Chlorinated-Solvent-Dependent Self-Sorting. Angew Chem Int Ed Engl 2023;62:e202217325. [PMID: 36625790 DOI: 10.1002/anie.202217325] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
26
Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023;299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023]  Open
27
Niitsu A, Sugita Y. Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Phys Chem Chem Phys 2023;25:3595-3606. [PMID: 36647771 DOI: 10.1039/d2cp03972a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
28
Díaz Vázquez G, Cui Q, Senes A. Thermodynamic analysis of the GASright transmembrane motif supports energetic model of dimerization. Biophys J 2023;122:143-155. [PMID: 36371634 PMCID: PMC9822795 DOI: 10.1016/j.bpj.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]  Open
29
Smalinskaitė L, Kim MK, Lewis AJO, Keenan RJ, Hegde RS. Mechanism of an intramembrane chaperone for multipass membrane proteins. Nature 2022;611:161-166. [PMID: 36261528 PMCID: PMC7614104 DOI: 10.1038/s41586-022-05336-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/12/2022] [Indexed: 01/29/2023]
30
Zhou C, Lu P. De novo design of membrane transport proteins. Proteins 2022;90:1800-1806. [DOI: 10.1002/prot.26336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 12/22/2022]
31
Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022;122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
32
Krishnan R S, Jana K, Shaji AH, Nair KS, Das AD, Vikraman D, Bajaj H, Kleinekathöfer U, Mahendran KR. Assembly of transmembrane pores from mirror-image peptides. Nat Commun 2022;13:5377. [PMID: 36104348 PMCID: PMC9474448 DOI: 10.1038/s41467-022-33155-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/05/2022] [Indexed: 11/18/2022]  Open
33
Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Nat Struct Mol Biol 2022;29:537-548. [PMID: 35655098 PMCID: PMC9809158 DOI: 10.1038/s41594-022-00775-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023]
34
Computational design of transmembrane proteins. Curr Opin Struct Biol 2022;74:102381. [DOI: 10.1016/j.sbi.2022.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/28/2022] [Accepted: 03/17/2022] [Indexed: 11/03/2022]
35
Puthumadathil N, Krishnan R S, Nair GS, Mahendran KR. Assembly of alpha-helical transmembrane pores through an intermediate state. NANOSCALE 2022;14:6507-6517. [PMID: 35420118 DOI: 10.1039/d2nr00556e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
36
Elazar A, Chandler NJ, Davey AS, Weinstein JY, Nguyen JV, Trenker R, Cross RS, Jenkins MR, Call MJ, Call ME, Fleishman SJ. De novo-designed transmembrane domains tune engineered receptor functions. eLife 2022;11:75660. [PMID: 35506657 PMCID: PMC9068223 DOI: 10.7554/elife.75660] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/14/2022] [Indexed: 12/20/2022]  Open
37
Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022;2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023]  Open
38
Interactions between Artificial Channel Protein, Water Molecules, and Ions Based on Theoretical Approaches. Symmetry (Basel) 2022. [DOI: 10.3390/sym14040691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
39
Corin K, Bowie JU. How physical forces drive the process of helical membrane protein folding. EMBO Rep 2022;23:e53025. [PMID: 35133709 PMCID: PMC8892262 DOI: 10.15252/embr.202153025] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/17/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022]  Open
40
Hegde RS. The Function, Structure, and Origins of the ER Membrane Protein Complex. Annu Rev Biochem 2022;91:651-678. [PMID: 35287476 DOI: 10.1146/annurev-biochem-032620-104553] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
41
Gaffney KA, Guo R, Bridges MD, Muhammednazaar S, Chen D, Kim M, Yang Z, Schilmiller AL, Faruk NF, Peng X, Jones AD, Kim KH, Sun L, Hubbell WL, Sosnick TR, Hong H. Lipid bilayer induces contraction of the denatured state ensemble of a helical-bundle membrane protein. Proc Natl Acad Sci U S A 2022;119:e2109169119. [PMID: 34969836 PMCID: PMC8740594 DOI: 10.1073/pnas.2109169119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/19/2022]  Open
42
Hong H, Choi HK, Yoon TY. Untangling the complexity of membrane protein folding. Curr Opin Struct Biol 2022;72:237-247. [PMID: 34995926 DOI: 10.1016/j.sbi.2021.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/15/2022]
43
Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021;232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Basu S, Assaf SS, Teheux F, Rooman M, Pucci F. BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021;1:742843. [PMID: 36303753 PMCID: PMC9581023 DOI: 10.3389/fbinf.2021.742843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022]  Open
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Amoozadeh S, Johnston J, Meisrimler CN. Exploiting Structural Modelling Tools to Explore Host-Translocated Effector Proteins. Int J Mol Sci 2021;22:12962. [PMID: 34884778 PMCID: PMC8657640 DOI: 10.3390/ijms222312962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022]  Open
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Sternke M, Tripp KW, Barrick D. Surface residues and non-additive interactions stabilize a consensus homeodomain protein. Biophys J 2021;120:5267-5278. [PMID: 34757081 DOI: 10.1016/j.bpj.2021.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]  Open
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Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proc Natl Acad Sci U S A 2021;118:e2103674118. [PMID: 34413192 PMCID: PMC8403937 DOI: 10.1073/pnas.2103674118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
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Zhou B, Wu Y, Su Z. Computational Simulation of Holin S105 in Membrane Bilayer and Its Dimerization Through a Helix-Turn-Helix Motif. J Membr Biol 2021;254:397-407. [PMID: 34189599 PMCID: PMC10811654 DOI: 10.1007/s00232-021-00187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/15/2021] [Indexed: 11/30/2022]
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Alford RF, Samanta R, Gray JJ. Diverse Scientific Benchmarks for Implicit Membrane Energy Functions. J Chem Theory Comput 2021;17:5248-5261. [PMID: 34310137 DOI: 10.1021/acs.jctc.0c00646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Woolfson DN. A Brief History of De Novo Protein Design: Minimal, Rational, and Computational. J Mol Biol 2021;433:167160. [PMID: 34298061 DOI: 10.1016/j.jmb.2021.167160] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
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