Dynamic Folding Pathway Models of the Trp-Cage Protein

Abstract

Using action-derived molecular dynamics (ADMD), we study the dynamic folding pathway models of the Trp-cage protein by providing its sequential conformational changes from its initial disordered structure to the final native structure at atomic details. We find that the numbers of native contacts and native hydrogen bonds are highly correlated, implying that the native structure of Trp-cage is achieved through the concurrent formations of native contacts and native hydrogen bonds. In early stage, an unfolded state appears with partially formed native contacts (~40%) and native hydrogen bonds (~30%). Afterward, the folding is initiated by the contact of the side chain of Tyr3 with that of Trp6, together with the formation of the N-terminal α-helix. Then, the C-terminal polyproline structure docks onto the Trp6 and Tyr3 rings, resulting in the formations of the hydrophobic core of Trp-cage and its near-native state. Finally, the slow adjustment processes of the near-native states into the native structure are dominant in later stage. The ADMD results are in agreement with those of the experimental folding studies on Trp-cage and consistent with most of other computational studies.

Potential of a Natural Deep Eutectic Solvent, Glyceline, in the Thermal Stability of the Trp-Cage Mini-protein

“…Previously reported studies ,,,− demonstrated that there are four factors which play a very crucial role in the stabilization of the Trp-cage mini-protein. These factors are (i) a stable hydrogen bond formation between Hϵ1 of the Trp6 residue and the backbone carbonyl (CO) of the Arg16 residue, (ii) the presence of a salt bridge between two residues Asp9 and Arg16, (iii) a hydrophobic core containing Tyr3, Leu7, Gly11, Pro12, Pro18, and Pro19 residues surrounding the central residue Trp6, and (iv) orientational preference of Trp6 indole plane with respect to other aromatic planes such as Tyr3, Pro12, Pro17, Pro18, and Pro19 in the hydrophobic core of the Trp-cage mini-protein.…”

Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy

“…The secondary structure of the folded protein includes a hydrophobic core formed around a central tryptophan (Trp) residue. , The protein tertiary structural motif includes an N-terminal α-helix, followed by a short 3 10 helix and a C-terminal PolyproIine II (PPII) helix. The hydrophobic core of the Trp-cage contains seven residues: Tyr3, Trp6, Leu7, Gly11, Pro12, Pro18, and Pro19. − The strong and compact hydrophobic core has been of great interest for theoretical and experimental studies. ,− ,− In addition, Hagen and co-workers have investigated the folding mechanism utilizing laser temperature jump (T-jump) to reveal a two-state folding process, which has been supported by several thermodynamic studies using differential scanning calorimetry and circular dichroism spectroscopy. − ,, Other studies ,, suggest the presence of a molten globule-like stable intermediate as well as an α-helical structure of the protein by utilizing fluorescence correlation spectroscopy and UV-resonance Raman spectroscopy. Hydrophobic contacts were originally found in the protein by NMR pulse-label-experiments.…”

“…By monitoring these types of changes around side-chain probes, detailed information about variations in the local structure can be captured. In particular, studies of the intrinsic behavior of the hydrophobic core region are difficult because of low solubility issues and the sensitivity of the core region to structural perturbations. ,, To observe these important side-chain interactions within proteins requires an IR reporter that is both sensitive to the forces at work within a hydrophobic core, i.e., hydrophobicity and electron repulsion often found in conjugated systems. The tyrosine ring mode has been developed and characterized as a site-specific IR probe that is extremely sensitive to these properties. , For example, the infrared bandwidth of this mode has been shown to change because of the electron-donating ability of the solvent combined with the hydrophobicity of the solvent.…”

“…In particular, studies of the intrinsic behavior of the hydrophobic core region are difficult because of low solubility issues and the sensitivity of the core region to structural perturbations. 9,24,45 To observe these important sidechain interactions within proteins requires an IR reporter that is both sensitive to the forces at work within a hydrophobic core, i.e., hydrophobicity and electron repulsion often found in conjugated systems. The tyrosine ring mode has been developed and characterized as a site-specific IR probe that is extremely sensitive to these properties.…”

Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage

“…Trp-cage is one of the most extensively studied model peptide systems in protein folding, − which has led to a fairly detailed understanding of its folding mechanism. For example, both experimental ,,,− and computational − ,,,,− ,,,, studies have shown that the α-helix is either partially or completely formed in the major folding transition state, often without the presence of many native tertiary stabilizing interactions.…”