Molecular Modeling of Enzymes Provides Unique Insights
Authors: Gdanski Rick 
Published: December 2007

Abstract
Enzymes are used in the oil industry as breakers for certain stimulation fluids. Although these proteins are quite useful, they are not well understood. The use of molecular modeling software to investigate chemical behavior and study proteins has been well established in the pharmaceutical industry. This type of software has recently been applied to chemistry problems faced in the oil industry. This paper will present the results of molecular dynamics calculations performed on two example enzymes: lysozyme and an exo-cellulase (CBH-I). The stability of the enzyme crevice containing the active site was studied for each of the enzymes as a function of temperature. The interaction or "docking" of a guar segment within the crevice was also studied and was found to be in qualitative agreement with classical expectations. Molecular dynamic calculations showed lysozyme should lose active site stability at about 175 F, which is in agreement with its known stability temperature. While a guar segment would readily dock with lysozyme, laboratory experiments proved lysozyme would not break guar. This result could be caused by improper alignment in the crevice (classical view), or it could be caused by the high affinity of the guar for the enzyme surface. The galactose side chains on guar may be too "sticky" to allow release of the broken backbone, resulting in the guar poisoning the enzyme.
Molecular dynamics of the exo-cellulase indicated possible stability of the enzyme crevice well above 150 F. However, this method does not probe hydrolytic stability at higher temperatures and therefore does not necessarily indicate continued enzymatic activity. The known stability temperature for CBH-I is about 150 F. Docking of a guar segment within the crevice provided insight into possible mechanisms involved in breaking fracturing gels. Comparisons with laboratory experiments were also made.

Introduction
Of the many oil industry technical problems that have been successfully solved, some of the solutions were discovered by trial and error and others involved scientific or engineering studies that provided enough detailed understanding that unexpected solutions could be found. These approaches have been successful for both mechanical and chemical problems. One of the more advanced techniques that has become available for studying chemical problems is molecular modeling or computational chemistry. Although the ultimate goal of molecular modeling is to be able to replace physical testing with computational testing, achieving this ultimate goal is not in the foreseeable future. However, molecular modeling can be very useful as a support tool for chemists seeking to gain a better understanding of a chemical system. This paper discusses the results of using molecular modeling to study the interactions of two enzymes with guar. These enzymes are not used in the oil industry but were quite useful in providing new information on how enzymes that are currently used in the oil industry might behave on a molecular level.

Molecular Modeling Theory
Software. The molecular modeling package for executing this study was QUANTA/CHARMm, which is a commercially available modeling software from MSI (Molecular Simulations, Inc.). QUANTA provided the graphical user interface and other tools for building and preparing models for calculations. CHARMm performed the calculations that drove the dynamics and minimizations. CHARMm is occasionally referred to as the "computational engine" for the package.
Molecular modeling centers around the calculation of the energy of the system. In simplified terms, the system energy can be thought of as being associated with internal and external parts, relative to the molecule. The internal part includes the bond energies, the torsional energies, bending energies, etc. The external part, or non-bonded part, includes the van der Waals interactions and electrostatic interactions.
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