REACTIVE SPECIES - Oxidation of Amino Acids, Peptides, and Proteins: Kinetics and Mechanism - page 9

generate ROS [73, 74, 74-77]. It has been suggested that ROS, produced by
silver nanoparticles, may disrupt the production of ATP and damage cell mem-
branes. The specific type of DNA damage or chromosomal aberrations needs
to be investigated. DNA damage response in silver nanoparticle-treated cells
by the upregulation of damage response proteins may be identified by conduct-
ing protein expression analysis [78]. Recently, there has been more emphasis
on protein-nanoparticle interactions for the development of functional and
safe nanoparticles [79]. Significantly, a role of modified fullerenes and cerium
oxide nanoparticles has been demonstrated in protecting mammalian cells
against damage, which can possibly be caused by ROS and RNS [80].
The biological consequences of various reactive species, mentioned above,
are determined by rates of their formation and decay in different intra- and
extracellular environments. Steady-state concentrations of reactive species can
be estimated using their reaction rates with various constituents of environ-
ments. Proteins are made of ∼70% of the mass of organic constituents related
to living matter and are an important target of reactive species. The modifica-
tions of proteins by reactive species are governed by factors such as structure,
redox properties, and acid-base chemistry of proteins [81]. At a molecular
level, assessing the protein structure is critical to understand the modifications
induced by oxidation processes and thus the function of proteins [82, 83]. The
next section describes the progress that has been made in revealing structures
of proteins. The role of redox properties of proteins in oxidative reactions is
explained for thiols as an example in Section 1.3.5. The influence of p K a and
the speciation of reactive amino acids and their moieties in proteins are pre-
sented in Chapter 2. Redox potentials, reaction rates, and oxidative mecha-
nisms of reactive species are given in Chapters 3-6. The involvement of reactive
species in environmental processes (e.g., disinfection and remediation) is also
presented in Section 1.4 and in Chapters 3-6.
1.2 PROTEIN STRUCTURE
The details of protein structure are very important in understanding bio-
chemical functions such as energy conversion, transport, enzyme catalysis, and
host defense [84, 85]. Studies on protein structure are also imperative to
understanding various in vivo processes, such as cell-cell communication,
ligand binding, folding, and transport of proteins across membranes [86-88].
A number of techniques have been applied to determine the structure of
proteins at all structural levels [87, 89-93]. Conformational changes in pro-
teins in response to alternations in the environment of a solvent can be
observed by using calorimetric and optical methods [94]. Optical methods
include UV-vis, infrared, and fluorescence spectroscopy, and circular dichro-
ism (CD), which have been applied in measuring protein thermodynamic
stabilities based on the denaturant-induced unfolding transition [95]. X-ray
crystallography has been used extensively to obtain high-resolution structural