Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Abstract

Terahertz absorption spectra of alanine polypeptides in water were simulated with classical molecular dynamics at 310 K. Vibrational modes and oscillator strengths were calculated based on a quasi-harmonic approximation. Absorption spectra of Ala n (n ¼ 5, 15, 30) with different chain lengths and Ala 15 in coiled and helical conformations were studied in 10 -40 cm 21 bandwidth. Simulation results indicated both the chain length and the conformation have significant influences on THz spectra of alanine polypeptides. With the increase of chain length, the average THz absorption intensity increases. Compared with the helical Ala 15 polypeptide, the THz spectra of coiled one shows stronger absorption peaks. These results were explained from different numbers of hydrogen bonds formed between polypeptides and the surrounding water molecules.

Detection of DNA oligonucleotides with base mutations by terahertz spectroscopy and microstructures

“…Since THz spectroscopy mainly manifests weak molecular interactions including primarily hydrogen bonds and van der Waals force, the number and intensity of hydrogen bonds are important factors influencing THz absorption intensity [ 44 , 45 ]. To understand the above detection results by the THz spectroscopies and the microstructures, MD simulations were performed to study the hydrogen bond behavior of these four oligonucleotide chains in aqueous solution.…”

Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy

“…At this point, the system contains 122 atoms of the peptide, 728 atoms of the aptamer, 68 Na + , 46 Cl -, as well as 17048 water molecules. The energy minimization, temperature and density equilibrium were followed in accordance with previous strategies and parameters for biological systems [31]. In this way, under standard atmospheric pressure (1.0 bar), the temperature was stable around 300 K, and the density relaxed to 1.003 g/cm −3 .…”

“…The THz absorption of MUC1 and random sequence in D-PBS is lower than that in PBS solution, owing to the conformational change of the random sequence in D-PBS solution. Videlicet, different conformations (such as flexible to rigid state [38] or coiled to helical state [31]) form diverse hydrogen bonds with water molecules, which will be mirrored by the variation of the THz absorption coefficients of the corresponding solutions.…”

“…Hydrogen bonds here are considered to have a donor-acceptor distance < 3.5 Å and an angle between donorhydrogen-acceptor > 135° [31,40,41]. We counted the hydrogen bonds between the MUC1 and anti-MUC1 aptamer, as well as between the biomolecules and surrounding water molecules during the entire binding simulation process (shown in Fig.…”

Preliminary investigation of Terahertz spectroscopy to predict pork freshness non-destructively

“…THz wave diversity makes many chemical molecules exhibit molecular motion characteristics in THz band different from other wavelengths. Biological macromolecules, such as amino acids (Li et al, 2017), peptides (Zhang et al, 2016), DNA (Zhang et al, 2013) and biological small molecules, such as nucleotides (Shen et al, 2003), can absorb THz wave due to molecule rotation, molecule vibration and overall vibration of molecular clusters. Therefore, polymeric biomaterials can be analyzed nondestructively by characteristic peaks and data of biomaterial THz spectra.…”