Statics of Biomacromolecules

Rathi, Prakash Chandra; Pfleger, Christopher; Klein, Doris L.; Gohlke, Holger

doi:10.1002/9783527636402.ch18

Cited by 4 publications

(7 citation statements)

References 101 publications

(132 reference statements)

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“…Constraint Network Analysis (CNA) predicts rigid and flexible regions within a biomolecule, which allows linking these static characteristics to the molecule’s stability and function [ 17 , 21 ]. CNA has been described in detail in refs.…”

Section: Methodsmentioning

confidence: 99%

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Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

et al. 2016

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Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability.

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Section: Methodsmentioning

confidence: 99%

“…CNA has been described in detail in refs. [ 17 , 21 , 35 , 76 ]. The approach has been used previously to predict the (thermodynamic) thermostability of proteins and to identify weak spot residues that, when mutated, are likely to improve thermostability [ 16 , 18 , 19 ].…”

Section: Methodsmentioning

confidence: 99%

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

et al. 2016

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“…The results revealed a sophisticated interplay between the static properties of the ribosomal exit tunnel and its functional role in cotranslational processes. The authors showed that considering flexibility characteristics of the antibiotics binding sites within the tunnel is required for explaining the observed binding selectivity of antibiotics . Further applications of rigidity analysis on RNA relate to the natural coarse‐graining of the structure, which is used for setting up simulations to generate conformational ensembles (see Rigidity Analysis to Coarse‐grain Biomolecules Prior to Conformational Sampling ).…”

Section: Applicationsmentioning

confidence: 99%

“…As to thermal stability, proteins from thermophilic organisms are generally less flexible than their mesophilic homologs . Therefore, understanding biomolecular flexibility and rigidity, and how they change due to binding of another molecule, mutations, temperature, or solvent, is instrumental both for a fundamental understanding of biomolecular function and with respect to protein engineering and ligand design …”

Section: Introductionmentioning

confidence: 99%

Rigidity theory for biomolecules: concepts, software, and applications

Hermans

Pfleger

Nutschel

et al. 2017

WIREs Comput Mol Sci

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The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous composition of flexible and rigid regions, which can aid in the understanding of biomolecular stability and long-ranged information transfer through biomolecules, and yield valuable information for rational drug design and protein engineering. We review fundamental concepts in rigidity theory, ways to represent biomolecules as constraint networks, and methodological and algorithmic developments for analyzing such networks and linking the results to biomolecular function. Software packages for performing rigidity analyses on biomolecules in an efficient, automated way are described, as are rigidity analyses on biomolecules including the ribosome, viruses, or transmembrane proteins. The analyses address questions of allosteric mechanisms, mutation effects on (thermo-)stability, protein (un-)folding, and coarse-graining of biomolecules. We advocate that the application of rigidity theory to biomolecules has matured in such a way that it could be broadly applied as a computational biophysical method to scrutinize biomolecular function from a structure-based point of view and to complement approaches focused on biomolecular dynamics. We discuss possibilities to improve constraint network representations and to perform large-scale and prospective studies.

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“…Here, we address the question of the relation between protein thermostability and structural rigidity by analyzing directly the static properties of a well-characterized set of 16 mutants of lipase A from Bacillus subtilis ( Bs LipA). We do so by applying the rigidity theory-based Constraint Network Analysis (CNA) approach developed by us [ 33 – 35 ], thereby considering the Bs LipA variants to be in static equilibrium, hence avoiding that the results depend on the temporal resolution of the approach.…”

Section: Introductionmentioning

confidence: 99%

Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis

2015

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Understanding the origin of thermostability is of fundamental importance in protein biochemistry. Opposing views on increased or decreased structural rigidity of the folded state have been put forward in this context. They have been related to differences in the temporal resolution of experiments and computations that probe atomic mobility. Here, we find a significant (p = 0.004) and fair (R 2 = 0.46) correlation between the structural rigidity of a well-characterized set of 16 mutants of lipase A from Bacillus subtilis (BsLipA) and their thermodynamic thermostability. We apply the rigidity theory-based Constraint Network Analysis (CNA) approach, analyzing directly and in a time-independent manner the statics of the BsLipA mutants. We carefully validate the CNA results on macroscopic and microscopic experimental observables and probe for their sensitivity with respect to input structures. Furthermore, we introduce a robust, local stability measure for predicting thermodynamic thermostability. Our results complement work that showed for pairs of homologous proteins that raising the structural stability is the most common way to obtain a higher thermostability. Furthermore, they demonstrate that related series of mutants with only a small number of mutations can be successfully analyzed by CNA, which suggests that CNA can be applied prospectively in rational protein design aimed at higher thermodynamic thermostability.

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Statics of Biomacromolecules

Cited by 4 publications

References 101 publications

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

Rigidity theory for biomolecules: concepts, software, and applications

Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis

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