Experimental and Computational Methods

As the availability of crystal structures increased in the early 1990s, a number of experimental and computational methods were developed to use the structure of the protein target as a route to discover novel hit compounds. The methods include de novo design, virtual screening, and fragment-based discovery. These developments are covered in more detail in the later chapters of this book, but their main features can be summarized as follows. 

Figure 1.2 Experimental and computational methods in molecular energetics. Illustration by Rui Alexandre.

The constant refinement of techniques for directed protein evolution also involves the development of increasingly sophisticated in silico tools. This co-evolution of experimental and computational methods enriches our toolkit for finding the sequence that fits. It is this mutual impact which makes ProSa a valuable component in designing both experiments and proteins. 

Vajda, S. and Guarnieri, F. (2006). Characterization of protein-ligand interaction sites using experimental and computational methods. Curr. Opin. Drug Discov. Dev. 9, 354—362. 

This chapter mainly focuses on the reactivity of 02 and its partially reduced forms. Over the past 5 years, oxygen isotope fractionation has been applied to a number of mechanistic problems. The experimental and computational methods developed to examine the relevant oxidation/reduction reactions are initially discussed. The use of oxygen equilibrium isotope effects as structural probes of transition metal 02 adducts will then be presented followed by a discussion of density function theory (DFT) calculations, which have been vital to their interpretation. Following this, studies of kinetic isotope effects upon defined outer-sphere and inner-sphere reactions will be described in the context of an electron transfer theory framework. The final sections will concentrate on implications for the reaction mechanisms of metalloenzymes that react with 02, 02 -, and H202 in order to illustrate the generality of the competitive isotope fractionation method. 

Recently, there has been considerable interest in determining thermochemical properties, such as the AH°( and EA values of carbenes, notably the halo- and dihalomethylenes, and both experimental and computational methods were applied to this end. One thorough ICR investigation produced heats of formation for CF2, CC12, CC1F, CFH and CC1H, from estimates of the thermochemistry of the proton transfer reaction of equation 44 where X and Y are F and/or Cl, and B is a base of known gas-phase basicity323. 

For many years, the oxygen reduction reaction (ORR) on Pt and Pt-based alloys has been studied extensively by experimental " and computational methods, and it has been shown that the formation of a Pt-skin layer is accompanied with a Pt-depleted layer underneath for many Pt-3d alloys. Notably, several studies of O adsorption on Pt-skin surfaces have revealed that the binding strength is weaker than that on the pure Pt(lll) surface and this may facilitate the removal of adsorbed O, therefore in-... 

Chapter 8—Molecular Interactions Learning from Protein Complexes The spectrum of interactions is critical to comprehending the dynamics of a living system, and understanding it can help to develop methodology for future studies in other systems. Rojas, de Juan, and Valencia review the current state of experimental and computational methods for the study of protein interactions, including prospects for future developments. 

Here we review the current state of experimental and computational methods for the study of protein interactions, including prospects for future developments. 

Extensive documentation of the accuracy of molecular mechanics calculations has been reported.For the most part, the discrepancies between experimental and calculated molecular geometries are within experimental error. Many of the systematic discrepancies in MM2, for example, have been documented. Some of the apparent errors can be associated with incorrect comparisons of bond lengths that are defined differently in various experimental and computational methods. The bond lengths have different numerical values because they are different physical quantities, rather than being real errors. Other problems have been attributed to a lack of accurate experimental data when the force field equations and parameters were formulated. 

Co(II) or Cu(II) histidine or imidazole complexes were immobilized in porous matrices (montmorillonite and MCM-41) via two methods (introduction of preformed complex or complex formation within the ion-exchanged host substances). It was found that immobilization in general and the latter method in particular increased catalytic activity and catalyst life time in the decomposition reactions of hydrogen peroxide relative to the matrix-free complexes. The immobilized materials were characterized by experimental and computational methods and the structures of the guest molecules inside the hosts were also investigated. 

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