ArticleProceedings of the National Academy of Sciences of the United States of America1999
Measures of residue density in protein structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Fine-Tuning of Alkaline Residues on the Hydrophilic Face Provides a Non-toxic Cationic α-Helical Antimicrobial Peptide Against Antibiotic-Resistant ESKAPE Pathogens.Frontiers in microbiology · 2021Article
- Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals.Life (Basel, Switzerland) · 2019Article
- Errors in protein synthesis increase the level of saturated fatty acids and affect the overall lipid profiles of yeast.PloS one · 2018Article
- Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.Acta crystallographica. Section D, Structural biology · 2017Article
- Protein stability: a crystallographer's perspective.Acta crystallographica. Section F, Structural biology communications · 2016Review
- Crystal structure and functional analysis of MiD49, a receptor for the mitochondrial fission protein Drp1.Protein science : a publication of the Protein Society · 2015Article
- The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis.Acta crystallographica. Section F, Structural biology communications · 2015Article
- MamA as a Model Protein for Structure-Based Insight into the Evolutionary Origins of Magnetotactic Bacteria.PloS one · 2015Article
- StableIsotope Labeling with Amino Acids in Cell Culture (SILAC)-based strategy for proteome-wide thermodynamic analysis of protein-ligand binding interactions.Molecular & cellular proteomics : MCP · 2014Article
- A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.Genetics · 2014Article
- Controlled apoptosis by a thermally toggled nanoscale amplifier of cellular uptake.Nano letters · 2014Article
- Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches.Cellular and molecular life sciences : CMLS · 2014Review
- Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?Genetics · 2013Article
- Article
- Folding without charges.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model.Journal of chemical theory and computation · 2011Article
- Structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans.Acta crystallographica. Section F, Structural biology and crystallization communications · 2011Article
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2 authors.
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Abstract
A hierarchy of residue density assessments and packing properties in protein structures are contrasted, including a regular density, a variety of charge densities, a hydrophobic density, a polar density, and an aromatic density. These densities are investigated by alternative distance measures and also at the interface of multiunit structures. Amino acids are divided into nine structural categories according to three secondary structure states and three solvent accessibility levels. To take account of amino acid abundance differences across protein structures, we normalize the observed density by the expected density defining a density index. Solvent accessibility levels exert the predominant influence in determinations of the regular residue density. Explicitly, the regular density values vary approximately linearly with respect to solvent accessibility levels, the linearity parameters depending on the amino acid. The charge index reveals pronounced inequalities between lysine and arginine in their interactions with acidic residues. The aromatic density calculations in all structural categories parallel the regular density calculations, indicating that the aromatic residues are distributed as a random sample of all residues. Moreover, aromatic residues are found to be over-represented in the neighborhood of all amino acids. This result might be attributed to nucleation sites and protein stability being substantially associated with aromatic residues.
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