原著和名: サガリバナ科名: サガリバナ科 = Lecythidaceae採集地: 台湾 恒春熱帯植物園 (台湾省 恒春熱帯植物園)採集日: 1968/8/9採集者: 萩庭丈壽整理番号: JH007629国立科学博物館整理番号: TNS-VS-95762

Boxue Tian (1334118)

C. Dale Poulter (641717)

Matthew P. Jacobson (174588)

PLoS Computational Biology

PubMed

a) Scatter plot of log(ncarbocation) versus the number of steps in the shortest reaction route from the linear substrate to the product skeletons. Red dots indicate skeletons that have products associated with EC numbers. The remaining skeletons (black) have not, to our knowledge, been observed in characterized monoterpenoid natural products. “step 1” is creation of the trans linear carbocation, and “step 2” represents trans/cis isomerization (which does not create cyclized skeletons). Therefore, cyclic skeletons are generated from “step 3”. b) Zoom-in view of the circled region in (a), with the structures of the skeletons depicted. For additional details, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005053#pcbi.1005053.s004" target="_blank">S3 Fig</a>.</p

FigShare

Defining the Product Chemical Space of Monoterpenoid Synthases - Fig 5

Boxue Tian

C. Dale Poulter

Matthew P. Jacobson

Crossref

Defining the Product Chemical Space of Monoterpenoid Synthases

Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements, making them particularly challenging for enzyme function prediction. To begin to address this challenge, we have developed a computational approach for the systematic enumeration of terpenoid carbocations. Application of this approach allows us to systematically define a nearly complete chemical space for the potential carbon skeletons of products from monoterpenoid synthases. Specifically, 18758 carbocations were generated, which we cluster into 74 cyclic skeletons. Five of the 74 skeletons are found in known natural products; some of the others are plausible for new functions, either in nature or engineered. This work systematizes the description of function for this class of enzymes, and provides a basis for predicting functions of uncharacterized enzymes. To our knowledge, this is the first computational study to explore the complete product chemical space of this important class of enzymes

C Dale Poulter

Matthew P Jacobson

Directory of Open Access Journals

Defining the Product Chemical Space of Monoterpenoid Synthases.

Tian, Boxue

Poulter, C Dale

Jacobson, Matthew P

eScholarship - University of California

English

<div>Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements, making them particularly challenging for enzyme function prediction. To begin to address this challenge, we have developed a computational approach for the systematic enumeration of terpenoid carbocations. Application of this approach allows us to systematically define a nearly complete chemical space for the potential carbon skeletons of products from monoterpenoid synthases. Specifically, 18758 carbocations were generated, which we cluster into 74 cyclic skeletons. Five of the 74 skeletons are found in known natural products; some of the others are plausible for new functions, either in nature or engineered. This work systematizes the description of function for this class of enzymes, and provides a basis for predicting functions of uncharacterized enzymes. To our knowledge, this is the first computational study to explore the complete product chemical space of this important class of enzymes.</div

https://figshare.com/articles/Defining_the_Product_Chemical_Space_of_Monoterpenoid_Synthases/3580131