Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

Jacobson, Matthew P.; Kalyanaraman, Chakrapani; Zhao, Suwen; Tian, Boxue

doi:10.1016/j.tibs.2014.05.006

Cited by 33 publications

(37 citation statements)

References 79 publications

(100 reference statements)

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“…Another fruitful direction is the integration of free energy sampling with automated and systematic reaction path search, 159,160 which may find great value in timely applications such as annotation of protein functions, 161 understanding of enzyme evolution 162,163 and design of novel enzymes. Finally, although we focused our discussions on solution and biological systems, the developments are also equally important to chemical processes in other complex environments, such as liquid/solid interfaces that are prevalent in materials science, heterogeneous catalysis and energy/environmental research.…”

Section: Discussionmentioning

confidence: 99%

QM/MM free energy simulations: recent progress and challenges

Dong

Ito

et al. 2016

Molecular Simulation

110

111

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Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections.

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Section: Discussionmentioning

confidence: 99%

QM/MM free energy simulations: recent progress and challenges

Dong

Ito

et al. 2016

Molecular Simulation

110

111

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“…53 While the current study fell short of establishing the exact function for SgcJ and its homologues, the structures of SgcJ and NCS-Orf16 and comparison to the NTF2-like superfamily of proteins allowed us to (i) define a putative substrate binding or catalytic active site, (ii) correlate the function of SgcJ to C-1027 biosynthesis by site-directed mutagenesis of the conserved residues lining this site, and (iii) propose that SgcJ and its homologues may play a catalytic role, along with other enediyne PKS associated enzymes, in transforming the linear polyene intermediate into an enzyme-sequestered 9-membered enediyne core intermediate. These findings will surely help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in 9-membered enediyne core biosynthesis in the future.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

et al. 2016

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Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in 9-membered enediyne core biosynthesis.

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“…This would circumvent the need for the prior specificity data and allow testing against any potential substrate. As reviewed by Jacobson et al . this virtual screening approach has been successful in predicting the substrates of enzymes in a number of other studies.…”

Section: Introductionmentioning

confidence: 99%

“…To be most useful, this virtual screening would be performed using homology models of the uncharacterised adenylation domains from cryptic NRPSs. Encouragingly, the use of homology models and virtual screening has been successfully employed for both drug discovery and substrate prediction in a number of cases as reviewed elsewhere . However, the accuracy of the homology models used can have a major impact on the success of virtual screening .…”

Section: Introductionmentioning

confidence: 99%

Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening

et al. 2015

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Nonribosomal peptide synthetases (NRPSs) synthesize a diverse array of bioactive small peptides, many of which are used in medicine. There is considerable interest in predicting NRPS substrate specificity in order to facilitate investigation of the many "cryptic" NRPS genes that have not been linked to any known product. However, the current sequence similarity-based methods are unable to produce reliable predictions when there is a lack of prior specificity data, which is a particular problem for fungal NRPSs. We conducted virtual screening on the specificity-determining domain of NRPSs, the adenylation domain, and found that virtual screening using experimentally determined structures results in good enrichment of the cognate substrate. Our results indicate that the conformation of the adenylation domain and in particular the conformation of a key conserved aromatic residue is important in determining the success of the virtual screening. When homology models of NRPS adenylation domains of known specificity, rather than experimentally determined structures, were built and used for virtual screening, good enrichment of the cognate substrate was also achieved in many cases. However, the accuracy of the models was key to the reliability of the predictions and there was a large variation in the results when different models of the same domain were used. This virtual screening approach is promising and is able to produce enrichment of the cognate substrates in many cases, but improvements in building and assessing homology models are required before the approach can be reliably applied to these models.

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Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

Cited by 33 publications

References 79 publications

QM/MM free energy simulations: recent progress and challenges

QM/MM free energy simulations: recent progress and challenges

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening

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