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.
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
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.
Inspect source passages
Calixarene docks dimethyllysine on lysozyme
These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.
Two crystal structures were refined at 1.9 and 2.2 Å.
Two almost identical structures (1.9 and 2.2 Å) were refined.
ESI-MS masses were 14,302.2 Da (lysozyme) and 14,498.0 Da (dimethylated).
Electrospray ionization mass spectrometry data (Waters LCT Premier XE) for lysozyme (14,302.2 Da) and dimethylated lysozyme (14,498.0 Da) indicated complete dimethylation of all six lysines and the N-terminus.
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.
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