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A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function

https://doi.org/10.1002/minf.201100087

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolution after Gene Duplication

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Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot

CHARMM: The biomolecular simulation program

inferredcites →https://doi.org/10.1002/prot.22488openalex-snapshot

Improved prediction of protein side‐chain conformations with SCWRL4

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Analysis and prediction of functional sub-types from protein sequence alignments

inferredcites →https://doi.org/10.1007/s00438-002-0709-yopenalex-snapshot

Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana

inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot

VMD: Visual molecular dynamics

inferredcites →https://doi.org/10.1016/j.abb.2005.10.011openalex-snapshot

Two pockets in the active site of maize sesquiterpene synthase TPS4 carry out sequential parts of the reaction scheme resulting in multiple products

inferredcites →https://doi.org/10.1016/j.cbpa.2007.12.008openalex-snapshot

Unearthing the roots of the terpenome

inferredcites →https://doi.org/10.1016/j.pbi.2006.03.014openalex-snapshot

Terpene synthases and the regulation, diversity and biological roles of terpene metabolism

inferredcites →https://doi.org/10.1016/j.phytochem.2009.07.030openalex-snapshot

Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants

inferredcites →https://doi.org/10.1016/s0009-2797(02)00165-5openalex-snapshot

An algorithm for identification and ranking of family-specific residues, applied to the ALDH3 family

inferredcites →https://doi.org/10.1016/s0031-9422(02)00080-8openalex-snapshot

Gene expression of 5-epi-aristolochene synthase and formation of capsidiol in roots of Nicotiana attenuata and N. sylvestris

inferredcites →https://doi.org/10.1016/s0076-6879(03)74020-8openalex-snapshot

Modeller: Generation and Refinement of Homology-Based Protein Structure Models

inferredcites →https://doi.org/10.1021/bi900483bopenalex-snapshot

Crystal Structure of (+)-δ-Cadinene Synthase from Gossypium arboreum and Evolutionary Divergence of Metal Binding Motifs for Catalysis

inferredcites →https://doi.org/10.1021/cb900295gopenalex-snapshot

Structural Elucidation of Cisoid and Transoid Cyclization Pathways of a Sesquiterpene Synthase Using 2-Fluorofarnesyl Diphosphates

inferredcites →https://doi.org/10.1021/cr00105a002openalex-snapshot

Enzymic formation of sesquiterpenes

inferredcites →https://doi.org/10.1021/cr050286wopenalex-snapshot

Structural Biology and Chemistry of the Terpenoid Cyclases

inferredcites →https://doi.org/10.1021/ja9005332openalex-snapshot

Consequences of Conformational Preorganization in Sesquiterpene Biosynthesis: Theoretical Studies on the Formation of the Bisabolene, Curcumene, Acoradiene, Zizaene, Cedrene, Duprezianene, and Sesquithuriferol Sesquiterpenes

inferredcites →https://doi.org/10.1021/ja993584hopenalex-snapshot

Demonstration of Germacrene A as an Intermediate in 5-Epi-aristolochene Synthase Catalysis

inferredcites →https://doi.org/10.1021/jp056965sopenalex-snapshot

Nonclassical Carbocations as C−H Hydrogen Bond Donors

inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

inferredcites →https://doi.org/10.1038/225563a0openalex-snapshot

Natural Selection and the Concept of a Protein Space

inferredcites →https://doi.org/10.1038/nature04607openalex-snapshot

Designed divergent evolution of enzyme function

inferredcites →https://doi.org/10.1038/nature05451openalex-snapshot

Empirical fitness landscapes reveal accessible evolutionary paths

inferredcites →https://doi.org/10.1038/nchembio.113openalex-snapshot

Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

inferredcites →https://doi.org/10.1038/nchembio.2007.5openalex-snapshot

The function of terpene natural products in the natural world

inferredcites →https://doi.org/10.1038/nchembio0408-217openalex-snapshot

Evolving biosynthetic tangos negotiate mechanistic landscapes

inferredcites →https://doi.org/10.1038/nrg1672openalex-snapshot

Missense meanderings in sequence space: a biophysical view of protein evolution

inferredcites →https://doi.org/10.1038/nrg2160openalex-snapshot

Mechanistic approaches to the study of evolution: the functional synthesis

inferredcites →https://doi.org/10.1038/nrg2482openalex-snapshot

Turning a hobby into a job: How duplicated genes find new functions

inferredcites →https://doi.org/10.1038/nrm2805openalex-snapshot

Exploring protein fitness landscapes by directed evolution

inferredcites →https://doi.org/10.1039/b601473aopenalex-snapshot

The dihydro-β-agarofuran sesquiterpenoids

inferredcites →https://doi.org/10.1039/b917107jopenalex-snapshot

The carbocation continuum in terpene biosynthesis—where are the secondary cations?

inferredcites →https://doi.org/10.1046/j.1365-313x.2003.01910.xopenalex-snapshot

Citrus fruit flavor and aroma biosynthesis: isolation, functional characterization, and developmental regulation of Cstps1, a key gene in the production of the sesquiterpene aroma compound valencene

inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot

Comparison of simple potential functions for simulating liquid water

inferredcites →https://doi.org/10.1073/pnas.0601605103openalex-snapshot

Identifying and manipulating structural determinates linking catalytic specificities in terpene synthases

inferredcites →https://doi.org/10.1073/pnas.95.8.4126openalex-snapshot

Plant terpenoid synthases: Molecular biology and phylogenetic analysis

inferredcites →https://doi.org/10.1074/jbc.270.13.7375openalex-snapshot

Cloning and Bacterial Expression of a Sesquiterpene Cyclase from Hyoscyamus muticus and Its Molecular Comparison to Related Terpene Cyclases

inferredcites →https://doi.org/10.1074/jbc.273.4.2078openalex-snapshot

Sesquiterpene Synthases from Grand Fir (Abies grandis)

inferredcites →https://doi.org/10.1074/jbc.m802682200openalex-snapshot

Protonation of a Neutral (S)-β-Bisabolene Intermediate Is Involved in (S)-β-Macrocarpene Formation by the Maize Sesquiterpene Synthases TPS6 and TPS11

inferredcites →https://doi.org/10.1093/bioinformatics/bth021openalex-snapshot

Phylogenomic inference of protein molecular function: advances and challenges

inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot

Clustal W and Clustal X version 2.0

inferredcites →https://doi.org/10.1093/genetics/158.2.811openalex-snapshot

Genomic Organization of Plant Terpene Synthases and Molecular Evolutionary Implications

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkp846openalex-snapshot

The Universal Protein Resource (UniProt) in 2010

inferredcites →https://doi.org/10.1104/pp.104.051318openalex-snapshot

The Biochemical and Molecular Basis for the Divergent Patterns in the Biosynthesis of Terpenes and Phenylpropenes in the Peltate Glands of Three Cultivars of Basil

inferredcites →https://doi.org/10.1104/pp.108.115824openalex-snapshot

Biochemical and Genomic Characterization of Terpene Synthases inMagnolia grandiflora

inferredcites →https://doi.org/10.1105/tpc.019877openalex-snapshot

The Variability of Sesquiterpenes Emitted from Two Zea mays Cultivars Is Controlled by Allelic Variation of Two Terpene Synthase Genes Encoding Stereoselective Multiple Product Enzymes

inferredcites →https://doi.org/10.1110/ps.062416606openalex-snapshot

Statistical potential for assessment and prediction of protein structures

inferredcites →https://doi.org/10.1126/science.1123348openalex-snapshot

Evolution of Hormone-Receptor Complexity by Molecular Exploitation

inferredcites →https://doi.org/10.1126/science.1123539openalex-snapshot

Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

inferredcites →https://doi.org/10.1126/science.1137786openalex-snapshot

Chimeras of Two Isoprenoid Synthases Catalyze All Four Coupling Reactions in Isoprenoid Biosynthesis

inferredcites →https://doi.org/10.1126/science.277.5333.1815openalex-snapshot

Structural Basis for Cyclic Terpene Biosynthesis by Tobacco 5-Epi-Aristolochene Synthase

inferredcites →https://doi.org/10.1371/journal.pcbi.1000002openalex-snapshot

How Protein Stability and New Functions Trade Off

inferredcites →https://doi.org/10.1371/journal.pcbi.1000621openalex-snapshot

Getting Started in Structural Phylogenomics

inferredcites →https://doi.org/10.1371/journal.pcbi.1001040openalex-snapshot

Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.phytochem.2020.112286zenodo-depositor-declared

Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity

inferred← citeshttps://doi.org/10.1016/j.cbpa.2012.02.002openalex-snapshot

Structure guided approaches toward exploiting and manipulating nonribosomal peptide and polyketide biosynthetic pathways

inferred← citeshttps://doi.org/10.1016/j.nexres.2026.101397openalex-snapshot

Comparative volatile chemical profiling of essential oil and headspace volatiles of Coleus malabaricus and related Coleus species using GC-MS and static HS-GC-MS analytical techniques

inferred← citeshttps://doi.org/10.1021/ja5066366openalex-snapshot

Evolutionary and Mechanistic Insights from the Reconstruction of α-Humulene Synthases from a Modern (+)-Germacrene A Synthase

inferred← citeshttps://doi.org/10.1039/c4cs00351aopenalex-snapshot

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

inferred← citeshttps://doi.org/10.1073/pnas.2218248120openalex-snapshot

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

inferred← citeshttps://doi.org/10.3389/fpls.2019.00177openalex-snapshot

Linking Terpene Synthases to Sesquiterpene Metabolism in Grapevine Flowers

inferred← citeshttps://doi.org/10.5936/csbj.201209018openalex-snapshot

FROM MOLECULAR PHYLOGENETICS TO QUANTUM CHEMISTRY: DISCOVERING ENZYME DESIGN PRINCIPLES THROUGH COMPUTATION

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