ArticleBMC structural biology2006
Prediction of transmembrane helix orientation in polytopic membrane proteins.
Article in BMC structural biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 90 citations in OpenAlex.
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- Challenges of Protein-Protein Docking of the Membrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- TMKit: a Python interface for computational analysis of transmembrane proteins.Briefings in bioinformatics · 2023Article
- Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.Computational and structural biotechnology journal · 2023Review
- Membrane contact probability: An essential and predictive character for the structural and functional studies of membrane proteins.PLoS computational biology · 2022Article
- Role of TRP ion channels in cerebral circulation and neurovascular communication.Neuroscience letters · 2021Review
- Endothelial CaThe Korean journal of physiology & pharmacology : official journal of the Korean Physiological Society and the Korean Society of Pharmacology · 2020Review
- Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces.Computational and structural biotechnology journal · 2020Article
- Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin.The Journal of biological chemistry · 2019Article
- Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain.Scientific reports · 2019Article
- Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints.Proteins · 2017Article
- Role of Ectopic Gene Conversion in the Evolution of aGenetics · 2017Article
- Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.BMC bioinformatics · 2017Article
- Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins.Journal of chemical information and modeling · 2016Article
- Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy.Nature communications · 2015Article
- Computational modeling of membrane proteins.Proteins · 2015Review
- The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing.Biochemistry · 2014Article
- Single-nucleotide evolution quantifies the importance of each site along the structure of mitochondrial carriers.Cellular and molecular life sciences : CMLS · 2014Article
- High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling.Bioinformatics (Oxford, England) · 2013Article
- Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.BMC bioinformatics · 2013Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMembrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins.
resultsWe present a method for prediction of the TM helix orientation, which is an essential step in ab initio modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS (LIPid-facing Surface), which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b6f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b6f structure from green alga but not the assignment of TM helices in the cyanobacterium b6f structure.
conclusionLIPS calculations can be used for the prediction of helix orientation in ab initio modeling of polytopic membrane proteins. We also show with the example of two cytochrome b6f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at http://gila.bioengr.uic.edu/lab/larisa/lips.html.
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