Minimum model for the alpha-helix-beta-hairpin transition in proteins

Computer Simulations of Peptides from the p53 DNA Binding Domain

We have studied the dynamics and thermodynamics of two of the four evolutionarily conserved segments from the p53 DNA binding domain, using molecular dynamics and replica exchange simulations. These two regions contain well-defined elements of secondary structure (a β hairpin for region II and an α helix for region V) and bind to DNA in the intact protein. They are also mutational hot spots. The goal of our study was to determine the stability and folding propensity of these peptides in isolation. We used three force fields and solvent models (CHARMM19 with EEF1, CHARMM27 with GBMV, GROMOS96 with SPC). The predicted stability, folding propensity, and secondary structures depend upon the potential. Secondary structure predictors identify helical propensity for region II, in agreement with one of the force fields (CHARMM/GBMV). However, the other two potentials favor β structure for this peptide, although the conformations may differ from the crystal. For region V secondary structure predictions are unclear. Only one force field (CHARMM/GBMV) produces low-lying free energy minima that retain some of the α helical structure from the crystal structure. The other two potentials appear to favor β structure for this peptide.

Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds

Pure Gō models (where every native interaction equally stabilizes the folded state) have widely proved their convenience in the computational investigation of protein folding. However, a chemistry-based description of the real interactions also provides a desirable tune in the analysis of the folding process, and thus some hybrid Gō potentials that combine both aspects have been proposed. Among all the noncovalent interactions that contribute to protein folding, hydrogen bonds are the only ones with a partial covalent character. This feature makes them directional and, thus, more difficult to model as part of the coarse-grained descriptions that are typically employed in Gō models. Thanks to a simplified but rigorous representation of backbone hydrogen bonds that we have recently proposed, we present in this article a combined potential (Gō + backbone hydrogen bond) to study the thermodynamics of protein folding in the frame of very simple simulation models. We show that the explicit inclusion of hydrogen bonds leads to a systematic improvement in the description of protein folding. We discuss a representative set of examples (from two-state folders to downhill proteins, with different types of native structures) that reveal a relevant agreement with experimental data.

Roles of non-native hydrogen-bonding interaction in helix-coil transition of a single polypeptide as revealed by comparison between Gō-like and non-Gō models

To explore the role of non-native interactions in the helix-coil transition, a detailed comparison between a Gō-like model and a non-Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō-like model, and the non-native ones with sequence interval more than 4 is also included into the non-Gō model. Some significant differences between the results from those two models have been found. The non-native hydrogen bonds were found most populated at temperature around the helix-coil transition. The rearrangement of non-native hydrogen bonds into native ones in the formation of alpha-helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non-Gō model for a non-short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non-native hydrogen bonds have complicated the temperature-dependence of Zimm-Bragg nucleation constant. The increase of relative probability of non-native hydrogen bonding for long polypeptide chains leads to non-monotonous chain length effect on the transition temperature.

The RCK1 domain of the human BKCa channel transduces Ca2+ binding into structural rearrangements

Large-conductance voltage- and Ca²⁺-activated K⁺ (BK_Ca) channels play a fundamental role in cellular function by integrating information from their voltage and Ca²⁺ sensors to control membrane potential and Ca²⁺ homeostasis. The molecular mechanism of Ca²⁺-dependent regulation of BK_Ca channels is unknown, but likely relies on the operation of two cytosolic domains, regulator of K⁺ conductance (RCK)1 and RCK2. Using solution-based investigations, we demonstrate that the purified BK_Ca RCK1 domain adopts an α/β fold, binds Ca²⁺, and assembles into an octameric superstructure similar to prokaryotic RCK domains. Results from steady-state and time-resolved spectroscopy reveal Ca²⁺-induced conformational changes in physiologically relevant [Ca²⁺]. The neutralization of residues known to be involved in high-affinity Ca²⁺ sensing (D362 and D367) prevented Ca²⁺-induced structural transitions in RCK1 but did not abolish Ca²⁺ binding. We provide evidence that the RCK1 domain is a high-affinity Ca²⁺ sensor that transduces Ca²⁺ binding into structural rearrangements, likely representing elementary steps in the Ca²⁺-dependent activation of human BK_Ca channels.