Thermal stability tuning without affecting gas-binding function of Thermochromatium tepidum cytochrome c'

Conformational rigidity of cytochrome c'-α from a thermophile is associated with slow NO binding

Cytochromes c'-α are nitric oxide (NO)-binding heme proteins derived from bacteria that can thrive in a wide range of temperature environments. Studies of mesophilic Alcaligenes xylosoxidans cytochrome c'-α (AxCP-α) have revealed an unusual NO-binding mechanism involving both heme faces, in which NO first binds to form a distal hexa-coordinate Fe(II)-NO (6cNO) intermediate and then displaces the proximal His to form a proximal penta-coordinate Fe(II)-NO (5cNO) final product. Here, we characterize a thermally stable cytochrome c'-α from thermophilic Hydrogenophilus thermoluteolus (PhCP-α) to understand how protein thermal stability affects NO binding. Electron paramagnetic and resonance Raman spectroscopies reveal the formation of a PhCP-α 5cNO product, with time-resolved (stopped-flow) UV-vis absorbance indicating the involvement of a 6cNO intermediate. Relative to AxCP-α, the rates of 6cNO and 5cNO formation in PhCP-α are ∼11- and ∼13-fold lower, respectively. Notably, x-ray crystal structures of PhCP-α in the presence and absence of NO suggest that the sluggish formation of the proximal 5cNO product results from conformational rigidity: the Arg-132 residue (adjacent to the proximal His ligand) is held in place by a salt bridge between Arg-75 and Glu-135 (an interaction not present in AxCP-α or a psychrophilic counterpart). Overall, our data provide fresh insights into structural factors controlling NO binding in heme proteins, including 5cNO complexes relevant to eukaryotic NO sensors.

Crystal structure of thermally stable homodimeric cytochrome c'-β from Thermus thermophilus

Cytochrome c'-β is a heme protein that belongs to the cytochrome P460 family and consists of homodimeric subunits with a predominantly antiparallel β-sheet fold. Here, the crystal structure of cytochrome c'-β from the thermophilic Thermus thermophilus (TTCP-β) is reported at 1.74 Å resolution. TTCP-β has a typical antiparallel β-sheet fold similar to that of cytochrome c'-β from the moderately thermophilic Methylococcus capsulatus (MCCP-β). The phenylalanine cap structure around the distal side of the heme is also similar in TTCP-β and MCCP-β, indicating that both proteins similarly bind nitric oxide and carbon monoxide, as observed spectroscopically. Notably, TTCP-β exhibits a denaturation temperature of 117°C, which is higher than that of MCCP-β. Mutational analysis reveals that the increased homodimeric interface area of TTCP-β contributes to its high thermal stability. Furthermore, 14 proline residues, which are mostly located in the TTCP-β loop regions, possibly contribute to the rigid loop structure compared with MCCP-β, which has only six proline residues. These findings, together with those from phylogenetic analysis, suggest that the structures of Thermus cytochromes c'-β, including TTCP-β, are optimized for function under the high-temperature conditions in which the source organisms live.

Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation

Agarase is a natural catalyst with a good prospect in the industry. However, most of the currently discovered β-agarases are unsuitable for relatively high-temperature and high-pressure conditions required by industrial production. In this study, molecular dynamics simulations were first used to investigate the dynamic changes of folding and unfolding of mesophile and thermophile β-agarases (i.e., 1URX and 3WZ1) to explore the thermostability mechanism at three high temperatures (300 K, 400 K, and 500 K). Results showed that the sequence identity of 3WZ1 and 1URX reaches 48.8%. 1URX has a higher thermal sensitivity and less thermostability than 3WZ1 as more thermostable regions and hydrogen bonds exist in 3WZ1 compared with 1URX. The structures of 1URX and 3WZ1 become unstable with increasing temperatures up to 500 K. The strategies to increase the thermostability of 1URX and 3WZ1 are discussed. This study could provide insights into the design and modification of β-agarases at a high temperature.