Biomedical subjects

Matthew J Realff

Publications and source records attributed to Matthew J Realff.

3 recordsLinked to original sources

PubMed2005

Simulation modeling of pooling for combinatorial protein engineering.

Pooling in directed-evolution experiments will greatly increase the throughput of screening systems, but important parameters such as the number of good mutants created and the activity level increase of the good mutants will depend highly on the protein being engineered. The authors developed and validated a Monte Carlo simulation model of pooling that allows the testing of various scenarios in silico before starting experimentation. Using a simplified test system of 2 enzymes, betagalactosidase (supermutant, or greatly improved enzyme) and beta-glucuronidase (dud, or enzyme with ancestral level of activity), the model accurately predicted the number of supermutants detected in experiments within a factor of 2. Additional simulations using more complex activity distributions show the versatility of the model. Pooling is most suited to cases such as the directed evolution of new function in a protein, where the background level of activity is minimized, making it easier to detect small increases in activity level. Pooling is most successful when a sensitive assay is employed. Using the model will increase the throughput of screening procedures for directed-evolution experiments and thus lead to speedier engineering of proteins.

Cells, Cultured↗

PubMed2005

Support vector machines for learning to identify the critical positions of a protein.

A method for identifying the positions in the amino acid sequence, which are critical for the catalytic activity of a protein using support vector machines (SVMs) is introduced and analysed. SVMs are supported by an efficient learning algorithm and can utilize some prior knowledge about the structure of the problem. The amino acid sequences of the variants of a protein, created by inducing mutations, along with their fitness are required as input data by the method to predict its critical positions. To investigate the performance of this algorithm, variants of the beta-lactamase enzyme were created in silico using simulations of both mutagenesis and recombination protocols. Results from literature on beta-lactamase were used to test the accuracy of this method. It was also compared with the results from a simple search algorithm. The algorithm was also shown to be able to predict critical positions that can tolerate two different amino acids and retain function.

Algorithms↗

PubMed2003

EcoWorx, Green Engineering principles in practice.

The 12 Principles of Green Engineering have been proposed as a framework within which to examine existing products and guide their redesign as well as to evaluate new product designs. The EcoWorx system represents a recyclable carpet tile product that is assessed using the 12 Principles of Green Engineering and cradle-to-cradle design principles to evaluate environmental, qualitative, and economic performance as compared to existing Shaw carpet tile products. The product design strategy embodies life cycle considerations of a cradle-to-cradle product that puts technical nutrient recovered materials into repeated use. EcoWorx offers a unique opportunity for Shaw to utilize the 12 Principles to analyze and optimize new products and processes for the additional capacity needed to meet rising demand for sustainable carpet products. The analysis of the EcoWorx system demonstrated the value of the 12 Principles in verifying and formalizing the experience and intuition of product designers. This suggests that the mistrial and error reliance on experience could be enhanced with this formalized approach and hence lead to more widespread success of design practices that result in sustainable products.

Conservation of Natural Resources↗