Conformation structural interpretation

In the present paper, we review recent work in our group that aimed at understanding the relationship between quantities that can be measured via SM FRET and the underlying conformational structure and dynamics of freely diffusing and surface-immobilized protein molecules. [54,55,65,66] Our approach differs from that employed by other researchers in order to interpret SM FRET measurements [49-53,67] in the following respects ... 

Since the dispersive properties of helices in what will be taken as the standard sense, now known to be right-handed as in myoglobin, have been the most thoroughly studied and since a case can be made that it is the predominant sense in proteins, this review will focus on the capacity of optical rotatory methods to discern mixtures of this conformation with disordered regions. It will discuss the manner in which theoretical considerations have provided the forms into which rotatory data are currently cast, the calibration of their constants by studies of synthetic polypeptides in known conformation, and then the application of these equations and scales in the structural interpretation of the rotatory dispersion of proteins. This pattern of analysis will undoubtedly undergo refinement and revision as these methods are applied to new species of polypeptide and protein in concert with other means of conformational assignment. In particular, an extension of the spectral range of measurement toward optically active absorption bands in the far ultraviolet can be expected to yield new information about the rotatory power of the peptide bond and thus enhance the interaction of theory and observation that has already proved fruitful. 

The study of the conformational behavior of polypeptides has intrinsic interest in a complex and challenging theoretical and experimental problem. There are also strong biological implications inasmuch as there are many known naturally occurring polypeptides, both linear and cyclic, with potent effects as hormones, toxins, antibiotics, and ionophores. It is very probable that these functions are closely related to the polymer chain conformations. Investigations of model polypepetides have been extremely useful for the interpretation of conformational behavior and for the elucidation of the interaction between proteins and other macromolecules. The conformational structures of polyproline and related compounds have been of particular interest due to the important role L-proline plays in effecting protein structure. 

The above analysis, shared by many spectroscopists in the field of small molecules, can be further expanded when vibrational spectroscopy is considered in the field of polymers and macromolecules in general. The wiggling of polymers adds new flavor to physics and chemistry. The translational periodicity of infinite polymers with perfect stmcture generates phonons and collective vibrations which give rise to absorption or Raman scattering bands that escape the interpretation based on the traditional spectroscopic correlations. The concept of collective motions forms the basis for the understanding of the vibrations of finite chain molecules which form a nonnegligible part of industrially relevant materials. On the other hand, real polymer samples never show perfect chemical, strereochemical, and conformational structure. Symmetry is broken and new bands appear which become characteristic of specific types of disorder. 

IR spectroscopy is another vibrational spectroscopic method used to determine the conformational structure of proteins and polypeptides. NIR spectroscopy provides little interpretable protein structural information because the broad bandwidth produces a severe overlap of most of the bands in the NIR spectra. As a consequence, the use of NIR is limited to basic structure determination in food components, and it has not been used for in-depth study of protein structural changes in muscle foods. On the other hand, mid-IR spectroscopy is a powerful tool for investigating the conformation of the polypeptide backbone of proteins. For these reasons, this chapter focuses on mid-IR spectroscopy. In mid-IR spectroscopy, the frequencies of amide I and amide II bands are very sensitive to protein conformation in food [18, 33, 34] and therefore to protein structural changes produced by thermal treatment [22]. 

The followmg types of studies will not be presented individually but may have contnbuted supportmg data to coverage by compound type conformational analyses [23 24, 25, 26 27], fluoropolymers [28, 29, 30 31, 32], solid-state NMR [ii], and solvent effects [34 35, 36, 37] Many excellent articles with m-depth NMR interpretation of one specific compound or of a small, structurally related group of compounds can be found in the chemical hterature A few of these, not incorporated elsewhere in this secUon are referenced here carbonyl fluondes [JS 39 40], fluoropropanes [41 42, 43], fluorocyclopropanes [44, 45 46], fluorobutanes [47], perfluorocyclobutanone [48], fluorohexanes [49], and vinyl fluondes [50, 51 52, 53, 54]... 

Indeed, cellular constituents or biomolecules must conform to the chemical and physical principles that govern all matter. Despite the spectacular diversity of life, the intricacy of biological structures, and the complexity of vital mechanisms, life functions are ultimately interpretable in chemical terms. Chemistry is the lo e of biolo eal phenomena. 

Much fewer experiments are available in solution where the few reported data are generally more concerned about the effect of molecular structure than about bond dissociation energy. In simple shear, it is generally agreed that chain flexibility dominantly influences the rate of bond scission, with the most rigid polymers being the easiest to fracture [157]. The results are interpreted in terms of the presence of good and poor sequences in the chain conformation. 

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