194
M. R. Nikolic et al.
proteins, and therefore improved access to additional low-abundance proteins. Ultimately, complete or near-complete sequences of novel PBPs could be deduced by
combined proteomics and de novo sequencing approaches (Nair et al. 2018).
8.9 Computational Studies of PBPs’ Structural
and Dynamics Properties
MDS and quantum mechanics/molecular mechanics (QM/MM) are valuable tools
for investigation of PBPs and their chromophores. These methods are useful for
explanation of spectroscopic and structural properties found by experimental data,
in addition to uncovering still controversial molecular mechanisms of energy transport in light-harvesting complexes. Several studies applied MDS to uncover the
effects of bound solvent molecules on the conformation of PCB and dynamic of PC
(Adir et al. 2002; Bellissent-Funel 2004). Waterman et al. (2014) investigated the
conformational response of PCB to the ability of solvents to form hydrogen bonds
using ab initio MDS of PCB in different solvents and ab initio calculations of NMR
chemical shift patterns. In order to understand long-lived quantum coherences in
PE, MDS, combined with quantum chemistry calculations, was employed to study
the coupling between the biological environment and the vertical excitation energies
of chromophores of PE antenna system (Aghtar et al. 2014). MDS was exploited
for monitoring of PCB conformational changes and HSA overall and individual
domain flexibility upon PCB binding to any of the two found binding sites on the
protein. MDS enabled refining these binding sites and supported experimental data
which demonstrate PCB-induced stabilization of HSA (Radibratovic et al. 2016).
MDS was a tool for comparison of conformational flexibility of PC from Arctic
cyanobacterial strain and mesophilic Arthrospira platensis in relation to cold adaptation (Su et al. 2017). The solvation dynamics of individual pigments in PC was
quantified using ab initio QM/MM nuclear dynamics (Blau et al. 2018), demonstrating how the molecular motion of PBP antennae funnel excitations to low-energy
pigments. QM/MM method was established for calculating the Raman spectra of
protein-bound chromophores and revealed the potential and limitations of QM calculations on isolated tetrapyrroles for determining the chromophore structures which
are not available (Mroginski et al. 2007). Elgabarty et al. (2013) presented hybrid
ab initio QM/MM MDS and theoretical NMR chemical shift calculations of PCB
in the binding pocket of the α-subunit of PC, unraveling the existence of dynamic
water channels in light-harvesting proteins.
M. R. Nikolic et al.
proteins, and therefore improved access to additional low-abundance proteins. Ultimately, complete or near-complete sequences of novel PBPs could be deduced by
combined proteomics and de novo sequencing approaches (Nair et al. 2018).
8.9 Computational Studies of PBPs’ Structural
and Dynamics Properties
MDS and quantum mechanics/molecular mechanics (QM/MM) are valuable tools
for investigation of PBPs and their chromophores. These methods are useful for
explanation of spectroscopic and structural properties found by experimental data,
in addition to uncovering still controversial molecular mechanisms of energy transport in light-harvesting complexes. Several studies applied MDS to uncover the
effects of bound solvent molecules on the conformation of PCB and dynamic of PC
(Adir et al. 2002; Bellissent-Funel 2004). Waterman et al. (2014) investigated the
conformational response of PCB to the ability of solvents to form hydrogen bonds
using ab initio MDS of PCB in different solvents and ab initio calculations of NMR
chemical shift patterns. In order to understand long-lived quantum coherences in
PE, MDS, combined with quantum chemistry calculations, was employed to study
the coupling between the biological environment and the vertical excitation energies
of chromophores of PE antenna system (Aghtar et al. 2014). MDS was exploited
for monitoring of PCB conformational changes and HSA overall and individual
domain flexibility upon PCB binding to any of the two found binding sites on the
protein. MDS enabled refining these binding sites and supported experimental data
which demonstrate PCB-induced stabilization of HSA (Radibratovic et al. 2016).
MDS was a tool for comparison of conformational flexibility of PC from Arctic
cyanobacterial strain and mesophilic Arthrospira platensis in relation to cold adaptation (Su et al. 2017). The solvation dynamics of individual pigments in PC was
quantified using ab initio QM/MM nuclear dynamics (Blau et al. 2018), demonstrating how the molecular motion of PBP antennae funnel excitations to low-energy
pigments. QM/MM method was established for calculating the Raman spectra of
protein-bound chromophores and revealed the potential and limitations of QM calculations on isolated tetrapyrroles for determining the chromophore structures which
are not available (Mroginski et al. 2007). Elgabarty et al. (2013) presented hybrid
ab initio QM/MM MDS and theoretical NMR chemical shift calculations of PCB
in the binding pocket of the α-subunit of PC, unraveling the existence of dynamic
water channels in light-harvesting proteins.