Proteins shapes

Peptides larger than 10 to 20 residues adopt conformations in solution through the interplay of hydrogen bonding, electrostatic and hydrophobic interactions, positioning of polar residues on the solvated surface of the polypeptide, and sequestering of hydrophobic residues in the nonpolar interior. Protein shape is dynamic, changing continuously in response to the solvent environment. The retention process in RPLC is initiated as the protein approaches the stationary-phase surface. Structured water associated at the phase surface and adjacent to hydrophobic contact surfaces on the polypeptide is released into the bulk mobile... 

HIC, like IEC, is performed under conditions that preserve protein shape and activity. It is used in preparative applications to obtain a selectivity complimentary to IEC and akin to RPLC but without the denaturing properties of the latter technique. Although HIC and RPLC share a mechanism based on hydro-phobic partitioning, the actual peak spacing and elution order of the two techniques can be different. This arises from the different hydrophobic contact points presented by the protein under native (HIC) and denaturing (RPLC) conditions. Although not widely used for analytical separations, HIC can be used to answer questions about accessible hydrophobic surface area that cannot be addressed by RPLC.44... 

As proteins emerge from ribosomes, they fold into three-dimensional conformations that are essential for their subsequent biologic activity. Generally, four levels of protein shape are distinguished ... 

Electrophoresis of proteins is generally carried out in gels made up of the cross-linked polymer polyacrylamide (Fig. 3-19). The polyacrylamide gel acts as a molecular sieve, slowing the migration of proteins approximately in proportion to their charge-to-mass ratio. Migration may also be affected by protein shape. In electrophoresis, the force moving the macromolecule is the electrical potential, E. The electrophoretic mobility of the molecule, g, is the ratio of the velocity of the par-... 

The structure of proteins determines their function and can be described on four levels, illustrated on page 447. The primary structure is the sequence of amino acids in the polypeptide chain. The secondary structure describes how various short portions of a chain are either wrapped into a coil called an alpha helix or folded into a thin pleated sheet. The tertiary structure is the way in which an entire polypeptide chain may either twist into a long fiber or bend into a globular clump. The quaternary structure describes how separate proteins may join to form one larger complex. Each level of structure is determined by the level before it, which means that ultimately it is the sequence of amino acids that creates the overall protein shape. Fhis final shape is maintained both by chemical bonds and by weaker molecular attractions between amino acid side groups. 

D. E. Koshland, Jr., Protein Shape and Biological Control," Scientific American, Oct. 1973. 

In spite of the fact that the a and /3 chains of hemoglobin are nonidentical with the myoglobin chain, the three-dimensional structures of all three chains are strikingly similar myoglobins and hemoglobins differ slightly in amino acid composition, depending on the species, but the protein shape remains essentially the same. 

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. 

In 2008 Ponomarenko et al. (36) developed the ElliPro Web server with approximation of the protein shape as ellipsoid. They implemented Thornton s method (15), which was originally developed for continuous epitopes and, together with protrusion index and neighboring residue clustering, allows the prediction of antibody epitopes in a given protein sequence or structure. 

The protein complex that carries out this reaction is called coupling factor or, more accurately, ATP synthase. ATP synthase is a complex of several proteins, shaped like a mushroom, with the cap on the stromal side of the thylakoid disc and the stalk going through the thylakoid... 

Usually, any positive interaction energy present in the X matrix is then set to 0 kcal mol Thus one focuses on the negative, favorable interaction energies and removes the information about small protein shape differences. Additionally, only using negative interaction energies allows a straightforward interpretation of the results. 

It does not matter that essentiality of some other elements (Na, K, Ca, Sr, Si) - if it actually refers to a certain element which cannot be replaced - will be unrelated to biocatalysis e.g., K can be fully replaced by Rb in many organisms (Scott and DeVoe 1954 Lwoff and Ionesco 1947), Ca roles, e.g. in control of cell budding can likewise be fulfilled by Sr and by various REE ions as a rule, while there are specific functions (unknown up to now) for Sr in corals and certain algae and for Ba in desmides, biocatalytic or not. Thus, neither K nor Ca are fundamental as single elements in such organisms. Examples for such different reasons of essentiality include electrolyte balances, changes of membrane permeability or protein shapes... 

Tel. 619-534-5100, e-mail ccms-request sdsc.edu, dem scripps.edu Complete package for solving X-ray crystal structures such as those of proteins. SHAPE for analyzing molecular surfaces. FLEX for displaying and animating molecular graphics. Sun, Silicon Graphics, and DEC (ULTRIX) workstations. 

Bonifacino IS, Lippincott-Schwartz J. Coat proteins shaping membrane transport. Nat. Rev. Mol. Cell Biol. 2003 4 409 14. LaPlante JM, Sun M, Falardeau J, Dai D, Brown EM, Slau-genhaupt SA, Vassilev PM. Lysosomal exocytosis is unpaired in mucolipidosis type IV. Mol. Genet. Metab. 2006 89 339-348. 

Determination of protein shape by photography with the electron microscope is of course, when it is feasible, the most direct method of determining the molecular dimensions. It has yielded vital information for some of the virus proteins and for certain other very large protein molecules. The evidence from electron microscope studies, however, cannot always be taken as final, for a preliminary drying of the protein preparation is essential before the photograph can be made, and the... 

Describe the three types of natural polymers, explain how amino-acid sequence determines protein shape, and thus function, draw small peptides, and use the sequence of one DNA strand to predict the sequence of the other ( 15.6) (EPs 15.68-15.79)... 

Protein shape, function, and amino acid sequence are interrelated. Which determines which ... 

Protein shapes are maintained by a variety of forces that arise from interactions between the amino-acid R groups. Name the amino acid that possesses each R group and the force that could arise in each of the following interactions ... 

Principles of restructuring meats were reviewed by Pearson and Dutson (1987). Basically, red or poultry meats are flaked or chunked into small pieces, mixed or tumbled with salt and polyphosphates to extract heat-coagulable protein, shaped into loaf pans... 

---