THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Abstract

Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster largescale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG) 3 . These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG) 3 . Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α-and β-domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors

“…For example in Fig. 4a, the peaks at approximately 150 cm −1 and 140 cm −1 in the dark-state spectrum are likely associated with interhelical and solvent-induced H-bonding interactions52. An analysis of the H-bonding dynamics of the intra- and interhelical fluctuations in both states of the receptor from the MD simulations reveal peaks at a similar frequency, further confirming our assignments (Table 1).…”

“…4a with the torsional oscillation of methyl groups of solvent-exposed helices in the receptor. From earlier experiments on other proteins4852 we have found that the experimentally determined 110 cm −1 peak is a general indicator of a flexible protein environment48. This supports our earlier notion that Meta II is more flexible than the dark-state receptor.…”

“…Hence, the vibrational analyses from the MD simulations carried out in this investigation combined with our previous studies on other proteins allow us to associate the experimentally observed peaks at about 120 cm −1 and 130 cm −1 in Fig. 4a with anharmonic, solvent-mediated fluctuations that couple to protein main-chain and backbone atoms, respectively485256. It is interesting to note that both solvent-mediated modes oscillate distinctly from the solvent-induced modes observed in the experimental dark-state spectrum.…”

Research of Ofloxacin Based on Terahertz Spectrum

“…Then the vibration frequency structure information of ofloxacin was obtained by Gaussian 03 software. The dynamic vibration of ofloxacin in THz band was observed by Gaussian View software [7] [8]. Experimental results do not appear virtual frequency phenomenon, consistent with the actual situation.…”

A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site

“…This family of models has been shown to successfully capture global protein conformational fluctuations including low frequency modes . For the protein used here, lysozyme, this includes the widely studied hinge‐bending motion . Although the ENM is most often employed for Normal Mode Analysis, it can also be used in molecular dynamics simulations …”