Model protein studies interpreted from

Step One for Energy Conversion in Mitochondria as Interpreted from Model Protein Studies... 

In protein crystals, due to the large size of the molecule, the empty space can have cross sections of 10-15 A or greater. The empty space between the protein molecules is occupied by mother liquor. This property of protein crystals, shared by nucleic acids and viruses, is otherwise unique among the crystal structures. In fact, the values of the packing coefficient of protein crystals range from 0.7 to 0.2, but the solvent molecules occupy the empty space so that the total packing coefficient is close to 1 [37]. Nevertheless, a detailed theoretical study has been carried out to examine the models of DNA-DNA molecular interactions on the basis of hard-sphere contact criteria. The hard-sphere computations are insufficient for qualitative interpretation of the packing of DNA helices in the solid state, but... 

This chapter focuses on experimental methods that have a symbiotic relationship with theoretical studies of proteins. In most cases, the need for simulations arises because the complexity of the internal motions that take place in proteins is such that the simple models used to interpret corresponding experiments on small molecules are not necessarily appropriate. From an analysis of the simulations, more realistic models can be constructed and parametrized in such a way that they can be fitted to the experimental data. Simulations can also serve to test approximations in the methods used to interpret the experiments and to provide additional information that makes it feasible to use the measurements in a new and interesting way. Examples of such applications of simulations to improve experimental analyses are given in this chapter. 

The broad aim of studying synthetic polypeptide model systems is to interpret better data obtained from studies of proteins and to design better experiments to gain new information about proteins. Protein studies using the polarization of fluorescence method have been reviewed recently by Weber (65), Steiner and Edelhoch (54) and Edelhoch and Steiner (16). 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

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