Chemical biology
Calixarene docks dimethyllysine on lysozyme
Open access · cc by · source: Europe PMC
p-Sulfonatocalix[4]arene selectively encapsulates Lys116-Me2 on dimethylated lysozyme, mimicking an aromatic cage.
Study at a glance
- Design
- Other — Crystal and NMR study of p-sulfonatocalix[4]arene bound to dimethylated lysozyme lysines
- N
- Protein–small-molecule structural study — no cohort N
- Population
- Dimethylated hen egg-white lysozyme with sclx4
- Outcome
- Site-selective Lys-Me2 encapsulation by the calixarene
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
Lys116-Me2 is encapsulated in the calixarene; NMR shows a large upfield NεMe shift; accessibility and nearby Arg/Asn contacts explain selectivity versus other lysines.
Methodology
Authors dimethylated hen lysozyme, solved sclx4 co-crystal structures, used 1H/13C NMR chemical shifts, and ran short MD at each Lys-Me2 site.
Limitations
No histone-tail co-crystal; MM-PBSA could not rank sites; precipitation limited solution stoichiometry.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
MD plus docking can design peptides that then meet a wet IC₅₀, which is a stronger claim than MD that cannot rank sites. SARS-CoV-2 Mpro peptides p12–p16 have IC₅₀ 3.11–5.36 μM; at 8-fold excess they cut s01 depletion from >98% to 70–95%; the ion-pair dyad lies 28.5 kJ mol⁻¹ above the neutral state. On dimethylated lysozyme, short MD at each Lys-Me₂ and a crystal of sclx4 encapsulating Lys116-Me₂ still left MM-PBSA unable to rank sites; precipitation limited solution stoichiometry.
Evidence for the claim as stated.
A short classical MD on a crystal pose can fail at ranking, while a neural-network AIMD-quality trajectory can propose a path. MM-PBSA could not rank lysozyme Lys-Me₂ sites; the Au(100) NNP metadynamics did propose an associative 0.3 eV ORR path — still without cations or bias. Success is Hamiltonian- and question-specific, not a property of 'having run MD'.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
A short classical MD on a crystal pose can fail at ranking, while a neural-network AIMD-quality trajectory can propose a path. MM-PBSA could not rank lysozyme Lys-Me₂ sites; the Au(100) NNP metadynamics did propose an associative 0.3 eV ORR path — still without cations or bias. Success is Hamiltonian- and question-specific, not a property of 'having run MD'.
- Supports · NN potentials map gold–water ORR paths
Related papers in this topic
Same topic cluster — not a recommendation engine.