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It is well known that there are some similarities among various naturally occurring amino acids. Thus, the complexity in protein systems could be reduced by sorting these amino acids with similarities into groups and then protein sequences can be simplified by reduced alphabets. This paper discusses how to group similar amino acids and whether there is a(More)
We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and(More)
Melittin, an amphipathic peptide from honeybee venom, consists of 26 amino acid residues and adopts different conformations from a random coil, to an alpha-helix, and to a self-assembled tetramer under certain aqueous environments. We report here our systematic studies of the hydration dynamics in these conformations using single intrinsic tryptophan (W19)(More)
We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three(More)
Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of(More)
Dynamic solvation at binding and active sites is critical to protein recognition and enzyme catalysis. We report here the complete characterization of ultrafast solvation dynamics at the recognition site of photoantenna molecule and at the active site of cofactor/substrate in enzyme photolyase by examining femtosecond-resolved fluorescence dynamics and the(More)
Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band(More)
Solubilities of deoxygenated sickle cell hemoglobin (deoxy-Hb S), at varying pH and temperature over a range of concentrations encompassing those found in erythrocytes, were measured. The technique involved ultracentrifugation, which gave values of the supernatant concentration and the mass of the sedimented material. The data establish that the solubility(More)
Flavoproteins are unique redox coenzymes, and the dynamic solvation at their function sites is critical to the understanding of their electron-transfer properties. Here, we report our complete characterization of the function-site solvation of holoflavodoxin in three redox states and of the binding-site solvation of apoflavodoxin. Using intrinsic flavin(More)
The effect of chemical structure of different biologically compatible S-nitrosothiols on the solvation environment at catalytic copper sites in a metal organic framework (MOF) suspended in a solution of ethanol is probed using computational methods. The use of a copper based MOF as a storage vehicle and catalyst (copper sites of the MOF) in the controlled(More)