Molecular Dynamics of Mesophilic-Like Mutants of a Cold-Adapted Enzyme: Insights into Distal Effects Induced by the Mutations

Networks and clusters of intramolecular interactions, as well as their “communication” across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme

RNA-Seq reveals a central role for lectin, C1q and von Willebrand factor A domains in the defensive glue of a terrestrial slug

<p>The tough, hydrogel glue produced by the slug <i>Arion subfuscus</i> achieves impressive performance through metal-based, protein cross-links. The primary sequence of these proteins was determined through transcriptome sequencing and proteome analysis by tandem mass spectrometry. The main proteins that correlate with adhesive function are a group of 11 small, highly abundant lectin-like proteins. These proteins matched the ligand-binding C-lectin, C1q or H-lectin domains. The variety of different lectin-like proteins and their potential for oligomerization suggests that they function as versatile and potent cross-linkers. In addition, the glue contains five matrilin-like proteins that are rich in von Willebrand factor A (VWA) and EGF domains. Both C-lectins and VWA domains are known to bind to ligands using divalent cations. These findings are consistent with the double network mechanism proposed for slug glue, with divalent ions serving as sacrificial bonds to dissipate energy.</p

Genetic Interaction between COMT and Dysbindin Effects Prefrontal Cortex Function During a BOLD fMRI Working Memory Paradigm

Background: Previous studies show that the catechol-O-methyltransferase (COMT) gene and the dysbindin (DTNBP1) gene impact prefrontal cortical function. Variations in these genes have been individually associated with prefrontal cortex (PFC) blood oxygenation level dependent (BOLD) fMRI during the N-back working memory task. To investigate epistasis suggested by animal studies, we used the COMT Val158Met (rs4680) polymorphism to condition a DTNBP1 SNP (rs9296985) that showed such an effect across several case-control schizophrenia cohorts (Papaleo et al., in preparation). Methodology: We studied 401 healthy Caucasians with valid COMT rs4680 and DTNBP1 rs9296985 genotypes and high-quality BOLD fMRI data from the 2-Back task at 3T. There were no significant differences in demographic variables or 2-back performance measures (accuracy/reaction time) across genotype groups. To model COMTxDTNBP1 interaction, in SPM5, we used full-factorial ANOVAs with age and gender as covariates of no interest. Results: In healthy subjects, we found evidence for an epistatic interaction between COMT-rs4680 and DTNBP1-rs9296985. We found that in subjects with COMT-Val158 homozygous backgrounds, those with rs9296985 T/T alleles were more inefficient than those with rs9296985 T/C alleles in PFC, specifically BA 9 & 46, FWE p<0.05 (corrected for a small volume; punc<0.000). We did not find this interaction for COMT-Met158 homozygotes Conclusion: By specifically modeling an interaction based on COMT-Val vs. COMT-Met conditioning, we found that DTNBP1-rs9296985 increased PFC inefficiency only for individuals homozygous for COMT-Val158. Where other data suggest gene x gene effects, it may be important to combine larger samples with statistically-derived models to fully capture epistatic interactions