ArticlePloS one2015
Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 86 citations in OpenAlex.
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- Amino Acids Frequency and Interaction Trends: Comprehensive Analysis of Experimentally Validated Viral Antigen-Antibody Complexes.Molecular biotechnology · 2026Article
- Multiscale Simulation of Phosphofructokinase-1 Assemblies: Capturing the Interplay between Specific and Transient Interactions.The journal of physical chemistry. B · 2025Article
- Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly.Nucleic acids research · 2025Article
- Elucidation of the Catalytic Apparatus and Mechanism of Human Chitotriosidase‑1.ACS catalysis · 2025Article
- Studying Noncovalent Interactions in Molecular Systems with Machine Learning.Chemical reviews · 2025Review
- Peptide Family Promotes Brain Cell Rejuvenation and Improved Cognition through Peripheral Delivery.ACS omega · 2025Article
- Enhancing implant surfaces: mechanical stability and cytocompatibility of DNase I coatings deposited by alternating current electrophoretic deposition.Frontiers in bioengineering and biotechnology · 2025Article
- A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational Ensembles.The journal of physical chemistry letters · 2024Article
- Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π-π, Cation-π, and CH-π Interactions.The journal of physical chemistry. B · 2024Article
- Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions.Journal of chemical theory and computation · 2024Article
- Understanding the Specific Implications of Amino Acids in the Antibody Development.The protein journal · 2024Review
- Supra-biological performance of immobilized enzymes enabled by chaperone-like specific non-covalent interactions.Nature communications · 2024Article
- Physical-Chemical Features Selection Reveals That Differences in Dipeptide Compositions Correlate Most with Protein-Protein Interactions.bioRxiv : the preprint server for biology · 2024Article
- Article
- Enhanced Activity and Stability of an Acetyl Xylan Esterase in Hydrophilic Alcohols through Site-Directed Mutagenesis.Molecules (Basel, Switzerland) · 2023Article
- Regulation of fungal raw-starch-degrading enzyme production depends on transcription factor phosphorylation and recruitment of the Mediator complex.Communications biology · 2023Article
- The anti-allergic potential of stingless bee honey from different botanical sources via modulation of mast cell degranulation.BMC complementary medicine and therapies · 2023Article
- A computational and laboratory approach for the investigation of interactions of peptide conjugated natural terpenes with EpHA2 receptor.Journal of molecular modeling · 2023Article
- Δ-Quantum machine-learning for medicinal chemistry.Physical chemistry chemical physics : PCCP · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesThree strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions.
methodsQuantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations.
resultsThe energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions.
conclusion(1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.
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