Coke deactivation of hydrotreating catalysts: A variable site model

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

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Evidence for a tandem two-site model of ligand binding to muscarinic acetylcholine receptors. Vol. 275 (2000) 18836-18844

Journal of Biological Chemistry ◽

10.1016/s0021-9258(20)77092-4 ◽

2004 ◽

Vol 279 (41) ◽

pp. 43361

Author(s):

Jan Jakubík ◽

Esam E. El-Fakahany ◽

Stanislav Tuček

Keyword(s):

Ligand Binding ◽

Acetylcholine Receptors ◽

Muscarinic Acetylcholine Receptors ◽

Muscarinic Acetylcholine ◽

Site Model

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Thermal Deactivation of Pd/CeO2–ZrO2 Three-Way Catalysts during Real Engine Aging: Analysis by a Surface plus Peripheral Site Model

ACS Omega ◽

10.1021/acsomega.0c04644 ◽

2020 ◽

Vol 5 (44) ◽

pp. 28897-28906

Author(s):

Ayumi Fujiwara ◽

Yutaro Tsurunari ◽

Hiroshi Yoshida ◽

Junya Ohyama ◽

Tatsuya Yamada ◽

...

Keyword(s):

Thermal Deactivation ◽

Site Model ◽

Peripheral Site

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Multi-image focus of attention for rapid site model construction

Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition ◽

10.1109/cvpr.1997.609383 ◽

2002 ◽

Cited By ~ 1

Author(s):

R.T. Collins

Keyword(s):

Focus Of Attention ◽

Model Construction ◽

Site Model ◽

Image Focus

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Structural and Spectroscopic Features of acis(Hydroxo)-FeIII-(Carboxylato) Configuration as an Active Site Model for Lipoxygenases

Inorganic Chemistry ◽

10.1021/ic0200040 ◽

2002 ◽

Vol 41 (21) ◽

pp. 5513-5520 ◽

Cited By ~ 41

Author(s):

Seiji Ogo ◽

Ryo Yamahara ◽

Mark Roach ◽

Tomoyoshi Suenobu ◽

Michihiko Aki ◽

...

Keyword(s):

Active Site ◽

Site Model ◽

Active Site Model

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Hydrogenolysis of Ethane on RH Powder. Application of the Landing Site Model

Bulletin des Sociétés Chimiques Belges ◽

10.1002/bscb.19890980106 ◽

2010 ◽

Vol 98 (1) ◽

pp. 49-62 ◽

Cited By ~ 2

Author(s):

A. Crucq ◽

L. Degols ◽

A. Frennet ◽

G. Lienard

Keyword(s):

Landing Site ◽

Site Model

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Unbinding of Hyaluronan Accelerates the Enzymatic Activity of Bee Hyaluronidase

Journal of Biological Chemistry ◽

10.1074/jbc.m111.263731 ◽

2011 ◽

Vol 286 (41) ◽

pp. 35699-35707 ◽

Cited By ~ 2

Author(s):

Attila Iliás ◽

Károly Liliom ◽

Brigitte Greiderer-Kleinlercher ◽

Stephan Reitinger ◽

Günter Lepperdinger

Keyword(s):

Experimental Data ◽

Quartz Crystal ◽

Surface Loop ◽

X Ray ◽

Site Model ◽

Substrate Interaction ◽

Close Proximity ◽

Binding Groove ◽

The One ◽

Best Fit

Hyaluronan (HA), a polymeric glycosaminoglycan ubiquitously present in higher animals, is hydrolyzed by hyaluronidases (HAases). Here, we used bee HAase as a model enzyme to study the HA-HAase interaction. Located in close proximity to the active center, a bulky surface loop, which appears to obstruct one end of the substrate binding groove, was found to be functionally involved in HA turnover. To better understand kinetic changes in substrate interaction, binding of high molecular weight HA to catalytically inactive HAase was monitored by means of quartz crystal microbalance technology. Replacement of the delimiting loop by a tetrapeptide interconnection increased the affinity for HA up to 100-fold, with a KD below 1 nm being the highest affinity among HA-binding proteins surveyed so far. The experimental data of HA-HAase interaction were further validated showing best fit to the theoretically proposed sequential two-site model. Besides the one, which had been shown previously in course of x-ray structure determination, a previously unrecognized binding site works in conjunction with an unbinding loop that facilitates liberation of hydrolyzed HA.

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