Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

Abstract

Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 10 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily.

Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics

“…Finally, it was pointed out that enzymes might possess evolutionary conserved dynamic traits, where, for example, RNase homologs with different biological functions, such as angiogenesis, anti-pathogenicity, immunosuppressivity, and highly efficient RNA cleavage, are not only grouped into evolutionarily distinct functional sub-families, but also show remarkable intra-subfamily conservation of dynamical properties evaluated by the quantitative characterization of the slowest modes of corresponding molecular dynamics (MD) simulations [107] that are not directly related to the conserved or semi-conserved features in the corresponding disorder profiles showing distribution of the per-residue disorder predisposition of these proteins [108]. These observations suggest that even for ordered globular proteins, in addition to the well-recognized structural conservation, which is a functionally important feature, functionality may also be linked to the evolutionarily conserved dynamical traits [107], which are only partially related to the conserved intrinsic disorder predisposition [108]. Therefore, such conservation of structural dynamics represents an important constituent of the evolutionary conservation of a functional protein fold [107,108].…”

“…These observations suggest that even for ordered globular proteins, in addition to the well-recognized structural conservation, which is a functionally important feature, functionality may also be linked to the evolutionarily conserved dynamical traits [107], which are only partially related to the conserved intrinsic disorder predisposition [108]. Therefore, such conservation of structural dynamics represents an important constituent of the evolutionary conservation of a functional protein fold [107,108].…”

Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily

“…The rate-limiting step was previously shown to correspond to a conformational change in a distal loop that is associated with the product release step in RNase A (Watt et al, 2011 ; Gagné and Doucet, 2013 ). The functional role of conformational exchange in product release was previously shown to rely on the movement of distal loop regions in RNase A, a hypothesis that we further extended to include functional RNase homologs sharing a conserved structural fold (Cole and Loria, 2002 ; Watt et al, 2007 ; Doucet et al, 2009 , 2011 ; Gagné et al, 2012 ; Gagné and Doucet, 2013 ; Narayanan et al, 2017 , 2018 ). Mutations of residues in these loop regions were shown to result in reduced rate constants for product release and lower substrate affinity, highlighting the role of these long-range motions in this enzyme (Gagné and Doucet, 2013 ).…”

“…In addition to their common ribonucleolytic function, the canonical RNases, henceforth referred to as subtypes , have evolved to perform other biological functions such as host defense, immunosuppressivity, angiogenesis, and anti-pathogenic activity, among others (Sorrentino, 2010 ). Further, the experimentally characterized human RNase subtypes display a wide range of substrate specificities (Boix et al, 2013 ), catalytic activities (Sorrentino, 2010 ; Gagné and Doucet, 2013 ) and conformational fluctuations on the millisecond timescale (Narayanan et al, 2017 , 2018 ). Efforts to relate specific conformational exchange events with ribonucleolytic function in this enzyme family is thus limited by the broader and often RNA-independent biological functions of many homologous RNase superfamily members.…”

How good are comparative models in the understanding of protein dynamics?

“…It is even more intriguing to observe differences in residue fluctuations of same protein under different conformational states . Hence, although global motions are conserved among proteins of same structural fold, each protein perhaps has its own characteristic dynamics that are determined by amino acid sequences as reflected from the observation of some differences in global motions of related proteins …”