ArticleFrontiers in molecular biosciences2021
3D Interaction Homology: Computational Titration of Aspartic Acid, Glutamic Acid and Histidine Can Create pH-Tunable Hydropathic Environment Maps.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- In silico evaluation of the anti Helicobacter pylori activity of selected bioactive compounds from Aloe vera.Scientific reports · 2025Article
- Enhancing Cold Adaptation of Bidomain Amylases by High-Throughput Computational Engineering.Angewandte Chemie (International ed. in English) · 2025Article
- The antimicrobial peptide Angie 5 inhibits TcdA and TcdB from Clostridioides difficile.Cellular and molecular life sciences : CMLS · 2025Article
- Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions.Journal of chemical theory and computation · 2024Article
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
- Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry.SLAS discovery : advancing life sciences R & D · 2023Review
- HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham.Frontiers in molecular biosciences · 2023Review
- 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins.Frontiers in molecular biosciences · 2023Article
- 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins.Current research in structural biology · 2021Article
- Systematized analysis of secondary structure dependence of key structural features of residues in soluble and membrane-bound proteins.Journal of structural biology: X · 2021Review
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2 authors.
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Abstract
Aspartic acid, glutamic acid and histidine are ionizable residues occupying various protein environments and perform many different functions in structures. Their roles are tied to their acid/base equilibria, solvent exposure, and backbone conformations. We propose that the number of unique environments for ASP, GLU and HIS is quite limited. We generated maps of these residue's environments using a hydropathic scoring function to record the type and magnitude of interactions for each residue in a 2703-protein structural dataset. These maps are backbone-dependent and suggest the existence of new structural motifs for each residue type. Additionally, we developed an algorithm for tuning these maps to any pH, a potentially useful element for protein design and structure building. Here, we elucidate the complex interplay between secondary structure, relative solvent accessibility, and residue ionization states: the degree of protonation for ionizable residues increases with solvent accessibility, which in turn is notably dependent on backbone structure.
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