L-tryptophan (l-Trp), a vital amino
acid for
the survival of various organisms, is synthesized by the enzyme tryptophan
synthase (TS) in organisms such as eubacteria, archaebacteria, protista,
fungi, and plantae. TS, a pyridoxal 5′-phosphate (PLP)-dependent
enzyme, comprises α and β subunits that typically form
an α2β2 tetramer. The enzyme’s
activity is regulated by the conformational switching of its α
and β subunits between the open (T state) and closed (R state)
conformations. Many microorganisms rely on TS for growth and replication,
making the enzyme and the l-Trp biosynthetic pathway potential
drug targets. For instance, Mycobacterium tuberculosis, Chlamydiae bacteria, Streptococcus pneumoniae, Francisella
tularensis, Salmonella bacteria, and Cryptosporidium parasitic
protozoa depend on l-Trp synthesis. Antibiotic-resistant salmonella strains have emerged, underscoring the
need for novel drugs targeting the l-Trp biosynthetic pathway,
especially for salmonella-related infections. A single amino acid
mutation can significantly impact enzyme function, affecting stability,
conformational dynamics, and active or allosteric sites. These changes
influence interactions, catalytic activity, and protein–ligand/protein–protein
interactions. This study focuses on the impact of mutating the βGln114
residue on the catalytic and allosteric sites of TS. Extensive molecular
dynamics simulations were conducted on E(PLP), E(AEX1),
E(A–A), and E(C3) forms of TS using the WT, βQ114A,
and βQ114N versions. The results show that both the βQ114A
and βQ114N mutations increase protein backbone root mean square
deviation fluctuations, destabilizing all TS forms. Conformational
and hydrogen bond analyses suggest the significance of βGln114
drifting away from cofactor/intermediates and forming hydrogen bonds
with water molecules necessary for l-Trp biosynthesis. The
βQ114A mutation creates a gap between βAla114 and cofactor/intermediates,
hindering hydrogen bond formation due to short side chains and disrupting
β-sites. Conversely, the βQ114N mutation positions βAsn114
closer to cofactor/intermediates, forming hydrogen bonds with O3 of
cofactors/intermediates and nearby water molecules, potentially disrupting
the l-Trp biosynthetic mechanism.