PubMed · 9824058
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L Brochard. 1998. Breathing: does regular mean normal?. https://doi.org/10.1097/00003246-199811000-00005
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Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information entropy, SΨ, a quantitative measure of the statistical variability in apolar and charged non-interacting surface (NIS) proportions across conformational ensembles. Within the Gibbs free-energy relation ΔG = ΔH - TΔS, SΨ is proposed as a computationally tractable entropic proxy rather than a direct thermodynamic observable or stand-alone estimator of binding affinity. Using energy-directed molecular docking via HADDOCK3 and explicit-solvent molecular dynamics simulations, it is demonstrated that favorable binding partners exhibit emergent, low-entropy N-states (discrete macrostates in NIS state space) indicative of preferential apolar/charged surface configurations. Across dozens of peptides and multiple receptor systems (WW, PDZ, and MDM2 domains), dominant N-states persisted under varied docking parameters and initial conditions. A meta-ensemble of 657 complexes from 36 experiments over 15 years confirmed the presence of dominant NIS modes independent of in silico methodology, suggesting an evolutionary selection pressure toward specific NIS fingerprints. These findings establish SΨ as a thermoinformatic descriptor that encodes favorable binding constraints into unique statistical signatures of the NIS.
Proton NMR spectra of short peptides with a glycyl (Gly) or N-methylglycyl (sarcosyl, Sar) residue were measured in various mixed solvents with a wide range of dielectric constants: 78.3-2.3. From analyses of the octet and quartet signals of the geminal alpha-protons of Gly and Sar residues, respectively, we have estimated chemical shift differences between the two alpha-protons, Delta delta(alpha/alpha'). It is found that the Delta delta(alpha/alpha') values increase with decreasing solvent polarity and the increasing rates depend significantly on amino acid sequences. By referring to infrared spectra and chemical shift of the terminal NH protons, deltaNH, of the peptides, the Delta delta(alpha/alpha') values were found to be a good probe of beta-turn formation. From solvent-dependent change of Delta delta(alpha/alpha'), we estimated the free energies for the beta-turn formation and compared the results with those estimated from deltaNH. Using the resulting free energies, we have discussed effects of solvent on the beta-turn formation.
We have previously shown that the distribution function describing the probability that a biological macromolecule picked at random has a particular enthalpy value can be calculated from the temperature dependence of the heat capacity of the macromolecule. The free energy as a function of enthalpy (free energy distribution) can then be determined from the enthalpy probability distribution. In addition, the free energy distribution at an arbitrary temperature can be calculated from the free energy distribution at a reference temperature. Here we apply this approach to a family of similar macromolecules, namely a set of transfer RNAs, specifically tRNA(Phe), tRNA(Val), tRNA(Met), tRNA(Ser), tRNA(Asp) and tRNA(Ile). Using published heat-capacity data, we calculate the enthalpy probability distribution functions for all of these molecules at five different temperatures covering the range from 30 to 80 degrees C. We then use these distributions to give a reference free-energy distribution, from which the thermodynamics at any temperature can be calculated for each species. We compare the reference free-energy distribution for the five tRNAs and find that, while the overall form of the distributions is similar, the local behavior of the functions varies considerably between the species.