Proteins molecular shape

Apart from tliese mainstream metliods enabling one to gain a comprehensive and detailed stmctural picture of proteins, which may or may not be in tlieir native state, tliere is a wide variety of otlier metliods capable of yielding detailed infonnation on one particular stmctural aspect, or comprehensive but lower resolution infonnation while keeping tlie protein in its native environment. One of tlie earliest of such metliods, which has recently undergone a notable renaissance, is analytical ultracentrifugation [24], which can yield infonnation on molecular mass and hence subunit composition and their association/dissociation equilibria (via sedimentation equilibrium experiments), and on molecular shape (via sedimentation velocity experiments), albeit only at solution concentrations of at least a few tentlis of a gram per litre. 

Molecular shape of the protein is not globular protein aggregates... 

Sweetness is a quality that defies definition, but whose complexity can be appreciated merely by examining the molecular structures of those compounds that elicit the sensation. They come in all molecular shapes and sizes, and they belong to such seemingly unrelated classes of compounds as aliphatic and aromatic organic compounds, amino acids, peptides and proteins, carbohydrates, complex glycosides, and even certain inorganic salts. 

This relatively small catalog of molecular shapes accounts for a remarkable number of molecules. Even complicated molecules such as proteins and other polymers have shapes that can be traced back to these relatively simple templates. The overall shape of a large molecule is a composite of the shapes associated with its inner atoms. The shape around each inner atom is determined by steric numbers and the number of lone pairs. 

In more recent years, additional progress and new computational methodologies in macromolecular quantum chemistry have placed further emphasis on studies in transferability. Motivated by studies on molecular similarity [69-115] and electron density representations of molecular shapes [116-130], the transferability, adjustability, and additivity of local density fragments have been analyzed within the framework of an Additive Fuzzy Density Fragmentation (AFDF) approach [114, 131, 132], This AFDF approach, motivated by the early charge assignment approach of Mulliken [1, 2], is the basis of the first technique for the computation of ab initio quality electron densities of macromolecules such as proteins [133-141],... 

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walters, P. (2002) The Shape and Structure of Proteins, Molecular Biology of the Cell, 4th edn. Garland Science, New York and London. 

Size-exclusion chromatography, also termed gel-permeation or gel-filtration chromatography, separates proteins on the basis of their size and shape. As most proteins fractionated by this technique are considered to have approximately similar molecular shape, separation is often described as being on the basis of molecular mass, although such a description is somewhat simplistic. 

The irreversible loss of a protein s native molecular shape is familiar to anyone who has boiled an egg. The white of an egg is largely a single protein called albumin. In a fresh egg, each albumin molecule is folded in a particular way that is its natural shape. This arrangement of each protein chain is stable at room temperature, but heat disrupts the interactions holding it together. At the temperature of boiling water the albumin unfolds, becoming a jumble... 

The relationship between molecular size and elution behavior can be used to estimate the molecular weight of an analyte. A calibration plot of log molecular weight (MW) vs. retention volume (or Ku) exhibits a linear segment between V, and Vi (Figure 7.1). If the plot is constructed with standard proteins with shapes similar to that of an analyte protein, the molecular weight of the analyte can be estimated by interpolation of its retention volume on the plot. The relationship between log MW and KD is linear for KD values between about 0.2 to 0.8. 

MOLECULAR SHAPE OE PROTEINS PRIMARY, SECONDARY AND TERTIARY STRUCTURES... 

Molecular shape of proteins primary, secondary and tertiary structures... 

The term secondary structure is used to describe the molecular shape or conformation of a molecule. The most important factor in determining the secondary structure of a material is its precise structure. For proteins, it is the amino acid sequence. Hydrogen bonding is also an important factor in determining the secondary structures of natural materials and those synthetic materials that can hydrogen-bond. In fact, for proteins, secondary structures are... 

The abnormal deposits found in the brains of CJD victims consist of an abnormal isoform of PrP. Prion protein is normally found in cells. Detailed structural studies show that normal cellular PrP (PrP ) is a soluble protein whose conformation is rich in a-helices with very little P-sheet. The PrP protein extracted from the brains of CJD victims (i.e., PrP ) is identical in primary amino acid sequence to the normal PrP (PrP ). However, PrP has a much greater content of P-sheet conformation with little a-helical structure. Thus PrP is neurotoxic because of its three-dimensional structure. When the prion protein is predominantly in an a-helical conformation it is nontoxic when the prion protein is predominantly in a P-sheet conformation, it kills neurons. The prion protein is thus made neurotoxic not by its amino acid composition but by its conformation. This concept is both fascinating and terrifying. Prion diseases are transmissible thus prions are infectious agents. However, prions are not like bacteria or viruses, or other infectious microbes—they are simply protein molecules. Prions are not microbes with cell membranes and nucleic acids they are not living things. Indeed, prions are not even infectious molecules, they are infectious molecular shapes. 

Two features that affect secondary protein structure (molecular shape) include the rigid, planar geometry and restricted rotation of the peptide bond, and interchain or intrachain hydrogen bonding of the type C=0-H-N. The a helix and the pleated sheet are common protein shapes. 

The etched liquid crystal modified capillaries were also tested for the separation of protein mixtures [32], For the two liquid crystal moieties investigated, similar separations of the protein mixtures were obtained. This result is not surprising since previous studies in HPLC have shown that liquid crystals are effective in discriminating between small molecules based on molecular shape [64-66]. The close association of the... 

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