MPtopo：一个膜蛋白拓扑结构数据库。
MPtopo: A database of membrane protein topology.
作者信息
Jayasinghe S, Hristova K, White S H
机构信息
Department of Physiology and Biophysics, University of California, Irvine, California 92697-4560, USA.
出版信息
Protein Sci. 2001 Feb;10(2):455-8. doi: 10.1110/ps.43501.
Abstract
The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.
摘要
标准序列数据库中膜蛋白（MP）跨膜（TM）序列分配的可靠性尚不确定，因为绝大多数是基于亲水性图谱。对于开发预测MP结构的新计算工具而言，一个具有可靠分配的MP数据库是必要的。因此，我们创建了MPtopo，这是一个MP数据库，其拓扑结构已通过晶体学、基因融合和其他方法进行了实验验证。使用MPtopo进行的测试有力地验证了四种现有的MP拓扑预测算法。MPtopo可通过互联网免费获取，并可通过基于SQL的搜索引擎进行查询。
相似文献
1
MPtopo: A database of membrane protein topology.MPtopo：一个膜蛋白拓扑结构数据库。
Protein Sci. 2001 Feb;10(2):455-8. doi: 10.1110/ps.43501.
2
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.β-桶状外膜蛋白拓扑结构预测方法的评估及一种共识预测方法
BMC Bioinformatics. 2005 Jan 12;6:7. doi: 10.1186/1471-2105-6-7.
3
4
ConPred_elite: a highly reliable approach to transmembrane topology predication.ConPred_elite：一种用于跨膜拓扑预测的高度可靠方法。
Comput Biol Chem. 2004 Feb;28(1):51-60. doi: 10.1016/j.compbiolchem.2003.11.002.
5
Energetics, stability, and prediction of transmembrane helices.跨膜螺旋的能量学、稳定性及预测
J Mol Biol. 2001 Oct 5;312(5):927-34. doi: 10.1006/jmbi.2001.5008.
6
Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction.评估跨膜拓扑结构预测方法中信号肽对拓扑结构预测的影响。
In Silico Biol. 2002;2(4):485-94.
7
8
THGS: a web-based database of Transmembrane Helices in Genome Sequences.THGS：一个基于网络的基因组序列跨膜螺旋数据库。
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D125-8. doi: 10.1093/nar/gkh130.
9
A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm.一种基于对SwissProt数据库进行统计分析的新型跨膜蛋白拓扑结构预测工具：OrienTM算法。
Protein Eng. 2001 Jun;14(6):387-90. doi: 10.1093/protein/14.6.387.
10
ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability.ConPred II：一种用于获得具有高可靠性跨膜拓扑模型的一致性预测方法。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W390-3. doi: 10.1093/nar/gkh380.
引用本文的文献
1
Amino acids hydrophobic properties in proteins are derived from their atomic polarities.蛋白质中氨基酸的疏水特性源于其原子极性。
Eur Biophys J. 2025 Jun 13. doi: 10.1007/s00249-025-01764-w.
2
His-tagged DM or DDM detergent micelles are reversibly conjugated by nickel ions.带有组氨酸标签的二肉豆蔻酰磷脂酰胆碱（DM）或二癸基磷脂酰胆碱（DDM）去污剂胶束通过镍离子进行可逆共轭。
Sci Rep. 2023 Oct 10;13(1):17138. doi: 10.1038/s41598-023-44236-x.
3
Three-stage model of helical membrane protein folding: Role of membrane-water interface as the intermediate stage vestibule for TM helices during their in membrano assembly.螺旋膜蛋白折叠的三阶段模型：膜-水界面作为 TM 螺旋在膜内组装过程中的中间阶段入口的作用。
Biochem Biophys Res Commun. 2022 Oct 8;624:1-7. doi: 10.1016/j.bbrc.2022.07.006. Epub 2022 Jul 6.
4
Spectroscopic evidence of tetanus toxin translocation domain bilayer-induced refolding and insertion.光谱证据表明破伤风毒素转位结构域双层诱导的重折叠和插入。
Biophys J. 2021 Nov 2;120(21):4763-4776. doi: 10.1016/j.bpj.2021.09.030. Epub 2021 Sep 21.
5
Expanding MPEx Hydropathy Analysis to Account for Electrostatic Contributions to Protein Interactions with Anionic Membranes.将 MPEx 疏水性分析扩展到考虑静电贡献对蛋白质与阴离子膜相互作用的影响。
J Membr Biol. 2021 Feb;254(1):109-117. doi: 10.1007/s00232-021-00170-5. Epub 2021 Feb 10.
6
The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins.色氨酸在生物学中的独特性：性质、代谢、相互作用及在蛋白质中的定位
Int J Mol Sci. 2020 Nov 20;21(22):8776. doi: 10.3390/ijms21228776.
7
GeTFEP: A general transfer free energy profile of transmembrane proteins.GeTFEP：一种跨膜蛋白的通用自由能转移图谱。
Protein Sci. 2020 Feb;29(2):469-479. doi: 10.1002/pro.3763. Epub 2019 Nov 11.
8
Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.α-螺旋跨膜蛋白结构测定的整合结构生物学
Structure. 2018 Apr 3;26(4):657-666.e2. doi: 10.1016/j.str.2018.02.006. Epub 2018 Mar 8.
9
Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule".重新审视跨膜区域附近的带电残基：“正内规则”被“负内耗尽/外富集规则”所补充。
BMC Biol. 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4.
10
Biological insertion of computationally designed short transmembrane segments.计算设计的短跨膜片段的生物插入。
Sci Rep. 2016 Mar 18;6:23397. doi: 10.1038/srep23397.
本文引用的文献
1
Structure of a glycerol-conducting channel and the basis for its selectivity.甘油传导通道的结构及其选择性的基础。
Science. 2000 Oct 20;290(5491):481-6. doi: 10.1126/science.290.5491.481.
2
Structural determinants of water permeation through aquaporin-1.水通道蛋白-1水渗透的结构决定因素。
Nature. 2000 Oct 5;407(6804):599-605. doi: 10.1038/35036519.
3
Crystal structure of rhodopsin: A G protein-coupled receptor.视紫红质的晶体结构：一种G蛋白偶联受体。
Science. 2000 Aug 4;289(5480):739-45. doi: 10.1126/science.289.5480.739.
4
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions.跨膜螺旋中氨基酸模式的统计分析：GxxxG基序频繁出现，并与相邻位置的β-分支残基相关联。
J Mol Biol. 2000 Feb 25;296(3):921-36. doi: 10.1006/jmbi.1999.3488.
5
The protein information resource (PIR).蛋白质信息资源（PIR）。
Nucleic Acids Res. 2000 Jan 1;28(1):41-4. doi: 10.1093/nar/28.1.41.
6
A simple method for predicting transmembrane alpha helices with better accuracy.一种预测跨膜α螺旋的简单方法，其准确性更高。
Protein Eng. 1999 Jul;12(7):557-61. doi: 10.1093/protein/12.7.557.
7
Membrane protein folding and stability: physical principles.膜蛋白折叠与稳定性：物理原理
Annu Rev Biophys Biomol Struct. 1999;28:319-65. doi: 10.1146/annurev.biophys.28.1.319.
8
Estimating loop-helix interfaces in a polytopic membrane protein by deletion analysis.
Biochemistry. 1999 Jun 29;38(26):8590-7. doi: 10.1021/bi990650j.
9
Transmembrane topology of human glucose 6-phosphate transporter.人葡萄糖6-磷酸转运蛋白的跨膜拓扑结构
J Biol Chem. 1999 May 14;274(20):13865-9. doi: 10.1074/jbc.274.20.13865.
10
Principles governing amino acid composition of integral membrane proteins: application to topology prediction.整合膜蛋白氨基酸组成的指导原则：在拓扑结构预测中的应用。
J Mol Biol. 1998 Oct 23;283(2):489-506. doi: 10.1006/jmbi.1998.2107.
Zotero 插件