Pressure Adaptations in Deep-Sea Moritella Dihydrofolate Reductases: Compressibility versus Stability

Abstract

Proteins from “pressure-loving” piezophiles appear to adapt by greater compressibility via larger total cavity volume. However, larger cavities in proteins have been associated with lower unfolding pressures. Here, dihydrofolate reductase (DHFR) from a moderate piezophile Moritella profunda (Mp) isolated at ~2.9 km in depth and from a hyperpiezophile Moritella yayanosii (My) isolated at ~11 km in depth were compared using molecular dynamics simulations. Although previous simulations indicate that MpDHFR is more compressible than a mesophile DHFR, here the average properties and a quasiharmonic analysis indicate that MpDHFR and MyDHFR have similar compressibilities. A cavity analysis also indicates that the three unique mutations in MyDHFR are near cavities, although the cavities are generally similar in size in both. However, while a cleft overlaps an internal cavity, thus forming a pathway from the surface to the interior in MpDHFR, the unique residue Tyr103 found in MyDHFR forms a hydrogen bond with Leu78, and the sidechain separates the cleft from the cavity. Thus, while Moritella DHFR may generally be well suited to high-pressure environments because of their greater compressibility, adaptation for greater depths may be to prevent water entry into the interior cavities.

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

“…The compressibility of proteins can be obtained from various methods: volumetric experiments, ultrasound velocity measurements, site selective hole burning, or fluorescence line narrowing spectroscopies [ 102 , 103 , 104 , 105 , 106 ]. There is a delicate balance in the proteins between the flexibility needed for the enzymatic activity and the rigidity needed for preserving the stable structure [ 20 ]. Interestingly, this balance is shifted in the case of thermotropic or barotropic enzymes to preserve the optimal flexibility in the preferred environment.…”

“…As mentioned earlier, high pressure naturally occurs in the biosystem, at the bottom of the deep sea. Understanding the adaptation to such an environment is also intensively examined [ 3 , 20 , 21 ].…”

Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures

“…In the deepest point of the ocean, one can experience more than 1.1 kbar (110 MPa) of pressure. Living organisms were observed in the deep sea, some of them were only barotolerant, but others were even barophilic organisms [ 41 , 42 , 43 ]. An investigation of the extreme environment has relevance in marine research and also in astrobiology [ 44 , 45 ].…”

The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface

“…A similar pattern has been shown for several enzymes. Dihydrofolate reductase (DHFR) is a necessary enzyme involved in the synthesis of purine and some amino acids, and it is therefore widespread within all microorganisms [ 26 , 71 , 72 ]. When Ohmae et al [ 25 ] examined the structural differences of DHFR between a piezosensitive E. coli strain and the piezophile Moritella profunda , they found that the structure of the enzymes from both strains overlapped almost perfectly.…”