Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Abstract

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties.

Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

“…Domains themselves have a strong tendency to fold ( Murzin et al, 1995 ), but although there is high structural modularity in a multidomain protein ( Han et al, 2007 ), the folding of a multidomain protein usually takes a more complex form than a simple sum of folding of individual domains ( Levy, 2017 ). The key component in the folding of a multidomain protein is the interaction of domain interfaces or linkers, which have been found to play nonuniversal roles in modulating folding stability ( Fast et al, 2009 ; Bhaskara et al, 2013 ; Vishwanath et al, 2018 ), cooperativity ( Batey et al, 2005 ) and kinetics ( Osváth et al, 2005 ; Batey et al, 2006 ; Batey and Clarke, 2006 ).…”

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

“…Sequences of 66 experimentally determined protein structures were selected as targets (section 2.1). Single chain and single‐domain proteins alone were considered to avoid the influence of protein‐protein and domain‐domain interactions on the accuracy of comparative models . For each of the targets, comparative models were built using single template as well as multiple templates (section 2.2).…”

Fold combinations in multi-domain proteins

“…Tethering of domains in multi-domain proteins confers folding, functional and stability advantages. For example, the folding rates of many multi-domain proteins are reported to be faster than the homologous single domain proteins 3, the stability of the multi-domain proteins is known to be better than the homologous single-domain proteins for many cases 4 and domain-domain interfaces are observed to play an important role in allosteric regulation of proteins 5-7. Multidomain proteins have evolved from single domain proteins through many duplication and adaptive events 3.…”