Recent advances in user-friendly computational tools to engineer protein function

Abstract

Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies

“…The new Zebra3D software complements our family of bioinformatic methods [52] that is being built around the Mustguseal protein alignment web-engine [39] and already includes sequence-based Zebra2/pocketZebra web-tools [14] , [79] to identify subfamily-specific determinants of functional diversity in protein sequences. We hope that a symbiosis of these tools will help to decipher the structure–function relationship, leading to the development of improved strategies for protein design and drug discovery [1] , [4] , [7] , [8] , [15] , [16] , [80] , [81] .…”

“…Bioinformatic analysis of “specific positions” in multiple sequence alignments – also known as subfamily/family-specific positions (SSPs) or specificity-determining positions (SDPs) – that are conserved only within subfamilies/families, but different among them, is a widely used class of computational approaches to study functional diversity in proteins [1] , [2] , [3] , [4] , [5] , [6] . Such SSPs/SDPs have both fundamental and practical value: they can help to understand how enzymes perform their natural functions, and can also be selected as hotspots for protein engineering experiments or as key residues involved in selective accommodation of ligand to assist drug discovery [7] , [8] .…”

FireProtDB: database of manually curated protein stability data

“…To provide our users with a more advanced description of their proteins of interest, we enriched the database by several important sequence- and structure-related information. These calculations were performed by HotSpot Wizard 3.0 ( 15 ), which is currently the only tool capable of deriving all these features in a single calculation ( 19 ) and provides machine-readable results. HotSpot Wizard was executed on a representative biological unit of each protein and provided the annotations for a structure, such as the residues located in protein pockets and tunnels, and a sequence, such as catalytic residues, evolutionary conservation scores, back-to-consensus mutations, and correlated pairs.…”

Web-based tools for computational enzyme design

“…Important computational tools for engineering enzyme function − among which is the goldstandard Rosetta toolbox [42] − have been reviewed [43,44]. Rosetta-based web tool FuncLib [13] [**] was specially designed to add multiple-point mutations to the binding site.…”