ArticleNucleic acids research2014
MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Conformational Flexibility of Transmembrane Helices: How it Works and Where it Matters.Chemical reviews · 2026Review
- Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Membrane properties that shape the evolution of membrane enzymes.Current opinion in structural biology · 2018Review
- Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.Proteins · 2018Article
- Approaches to ab initio molecular replacement of α-helical transmembrane proteins.Acta crystallographica. Section D, Structural biology · 2017Article
- SL2: an interactive webtool for modeling of missing segments in proteins.Nucleic acids research · 2016Article
- NGL Viewer: a web application for molecular visualization.Nucleic acids research · 2015Article
- Structure and mechanism of cysteine peptidase gingipain K (Kgp), a major virulence factor of Porphyromonas gingivalis in periodontitis.The Journal of biological chemistry · 2014Article
- Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes.Journal of biomolecular NMR · 2014Article
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4 authors.
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Abstract
The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP:PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.
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