Neutral genetic drift can aid functional protein evolution

BACKGROUND: Many of the mutations accumulated by naturally evolving proteins are neutral in the sense that they do not significantly alter a protein's ability to perform its primary biological function. However, new protein functions evolve when selection begins to favor other, "promiscuous" functions that are incidental to a protein's biological role. If mutations that are neutral with respect to a protein's primary biological function cause substantial changes in promiscuous functions, these mutations could enable future functional evolution. RESULTS: Here we investigate this possibility experimentally by examining how cytochrome P450 enzymes that have evolved neutrally with respect to activity on a single substrate have changed in their abilities to catalyze reactions on five other substrates. We find that the enzymes have sometimes changed as much as four-fold in the promiscuous activities. The changes in promiscuous activities tend to increase with the number of mutations, and can be largely rationalized in terms of the chemical structures of the substrates. The activities on chemically similar substrates tend to change in a coordinated fashion, potentially providing a route for systematically predicting the change in one function based on the measurement of several others. CONCLUSIONS: Our work suggests that initially neutral genetic drift can lead to substantial changes in protein functions that are not currently under selection, in effect poising the proteins to more readily undergo functional evolution should selection "ask new questions" in the future

Random Field Model Reveals Structure of the Protein Recombinational Landscape

We are interested in how intragenic recombination contributes to the evolution of proteins and how this mechanism complements and enhances the diversity generated by random mutation. Experiments have revealed that proteins are highly tolerant to recombination with homologous sequences (mutation by recombination is conservative); more surprisingly, they have also shown that homologous sequence fragments make largely additive contributions to biophysical properties such as stability. Here, we develop a random field model to describe the statistical features of the subset of protein space accessible by recombination, which we refer to as the recombinational landscape. This model shows quantitative agreement with experimental results compiled from eight libraries of proteins that were generated by recombining gene fragments from homologous proteins. The model reveals a recombinational landscape that is highly enriched in functional sequences, with properties dominated by a large-scale additive structure. It also quantifies the relative contributions of parent sequence identity, crossover locations, and protein fold to the tolerance of proteins to recombination. Intragenic recombination explores a unique subset of sequence space that promotes rapid molecular diversification and functional adaptation

Exploring protein fitness landscapes by directed evolution

Directed evolution circumvents our profound ignorance of how a protein's sequence encodes its function by using iterative rounds of random mutation and artificial selection to discover new and useful proteins. Proteins can be tuned to adapt to new functions or environments by simple adaptive walks involving small numbers of mutations. Directed evolution studies have shown how rapidly some proteins can evolve under strong selection pressures and, because the entire 'fossil record' of evolutionary intermediates is available for detailed study, they have provided new insight into the relationship between sequence and function. Directed evolution has also shown how mutations that are functionally neutral can set the stage for further adaptation

Navigating the protein fitness landscape with Gaussian processes

Knowing how protein sequence maps to function (the “fitness landscape”) is critical for understanding protein evolution as well as for engineering proteins with new and useful properties. We demonstrate that the protein fitness landscape can be inferred from experimental data, using Gaussian processes, a Bayesian learning technique. Gaussian process landscapes can model various protein sequence properties, including functional status, thermostability, enzyme activity, and ligand binding affinity. Trained on experimental data, these models achieve unrivaled quantitative accuracy. Furthermore, the explicit representation of model uncertainty allows for efficient searches through the vast space of possible sequences. We develop and test two protein sequence design algorithms motivated by Bayesian decision theory. The first one identifies small sets of sequences that are informative about the landscape; the second one identifies optimized sequences by iteratively improving the Gaussian process model in regions of the landscape that are predicted to be optimized. We demonstrate the ability of Gaussian processes to guide the search through protein sequence space by designing, constructing, and testing chimeric cytochrome P450s. These algorithms allowed us to engineer active P450 enzymes that are more thermostable than any previously made by chimeragenesis, rational design, or directed evolution

In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ

Directed evolution continues to expand the capabilities of complex biomolecules for a range of applications, such as adeno-associated virus vectors for gene therapy; however, advances in library design and selection strategies are key to develop variants that overcome barriers to clinical translation. To address this need, we applied structure-guided SCHEMA recombination of the multimeric adeno-associated virus (AAV) capsid to generate a highly diversified chimeric library with minimal structural disruption. A stringent in vivo Cre-dependent selection strategy was implemented to identify variants that transduce adult neural stem cells (NSCs) in the subventricular zone. A novel variant, SCH9, infected 60% of NSCs and mediated 24-fold higher GFP expression and a 12-fold greater transduction volume than AAV9. SCH9 utilizes both galactose and heparan sulfate as cell surface receptors and exhibits increased resistance to neutralizing antibodies. These results establish the SCHEMA library as a valuable tool for directed evolution and SCH9 as an effective gene delivery vector to investigate subventricular NSCs

Chemical and structural characterization of SeIV biotransformations by Stenotrophomonas bentonitica into Se0 nanostructures and volatiles Se species

Microorganisms such as Stenotrophomonas bentonitica could influence the safety of the deep geological repository system by producing nanoparticles and volatile compounds of selenium

Uniformly Accelerated Charge in a Quantum Field: From Radiation Reaction to Unruh Effect

We present a stochastic theory for the nonequilibrium dynamics of charges moving in a quantum scalar field based on the worldline influence functional and the close-time-path (CTP or in-in) coarse-grained effective action method. We summarize (1) the steps leading to a derivation of a modified Abraham-Lorentz-Dirac equation whose solutions describe a causal semiclassical theory free of runaway solutions and without pre-acceleration patholigies, and (2) the transformation to a stochastic effective action which generates Abraham-Lorentz-Dirac-Langevin equations depicting the fluctuations of a particle's worldline around its semiclassical trajectory. We point out the misconceptions in trying to directly relate radiation reaction to vacuum fluctuations, and discuss how, in the framework that we have developed, an array of phenomena, from classical radiation and radiation reaction to the Unruh effect, are interrelated to each other as manifestations at the classical, stochastic and quantum levels. Using this method we give a derivation of the Unruh effect for the spacetime worldline coordinates of an accelerating charge. Our stochastic particle-field model, which was inspired by earlier work in cosmological backreaction, can be used as an analog to the black hole backreaction problem describing the stochastic dynamics of a black hole event horizon.Comment: Invited talk given by BLH at the International Assembly on Relativistic Dynamics (IARD), June 2004, Saas Fee, Switzerland. 19 pages, 1 figur

Effect of feeding cows with unsaturated fatty acid sources on milk production, milk composition, milk fatty acid profile, and physicochemical and sensory characteristics of ice cream

Simple Summary: The objective of this study was to evaluate the effects of supplementation of dairy cows' diets with different fatty acid (FA) sources on milk production, milk composition, milk fatty acid profile, and physicochemical and sensory characteristics of ice cream. Supplementation (3% dry matter (DM)) of diets with soybean oil (SO) and fish oil (FO) did not have detrimental effects on milk production, milk composition, or ice cream physicochemical and sensory characteristics. From a human standpoint, SO and FO improved the FA profile of milk. Abstract: The objective of this study was to evaluate the effects of supplementation of dairy cows with different fatty acid sources (soybean oil (SO) and fish oil (FO)) on milk production, milk composition, milk fatty acid profile, and physicochemical and sensory characteristics of ice cream. During 63 days, fifteen Holstein cows averaging 198 ± 35 days in milk were assigned to three groups: control diet with no added lipid (n = 5 cows); and supplemented diets with SO (n = 5 cows; unrefined SO; 30 g/kg DM) or FO (n = 5 cows; FO from unrefined salmon oil; 30 g/kg DM). Milk production, milk fat, and milk protein were not affected by treatments. Saturated fatty acids in milk fat were decreased with SO and FO compared with control. C18:2 cis-9, cis-12 was increased with SO whereas C18:2 cis-9, trans-11, C20:3n-3, C20:3n-6, C20:5n-3, and C22:6n-3 were the highest with FO. Draw temperature and firmness were higher in SO compared to control and FO ice creams. Melting resistance was higher in FO compared with control and SO ice creams. Supplementation of cow diets with SO and FO did not have detrimental effects on milk production, or ice cream physicochemical and sensory characteristics

Franck-Condon-Broadened Angle-Resolved Photoemission Spectra Predicted in LaMnO3

The sudden photohole of least energy created in the photoemission process is a vibrationally excited state of a small polaron. Therefore the photoemission spectrum in LaMnO3 is predicted to have multiple Franck-Condon vibrational sidebands. This generates an intrinsic line broadening approximately 0.5 eV. The photoemission spectral function has two peaks whose central energies disperse with band width approximately 1.2 eV. Signatures of these phenomena are predicted to appear in angle-resolved photoemission spectra.Comment: Revtex file 4 pages and 3 figure