M protein

Brooks III, C. L., Karplus, M., Pettitt, B. M. Proteins A Theoretical Perspective of Dynamics, Structure and Thermodynamics. Advances in Chemical Physics, vol. LXXI. John Wiley Sons, New York, 1988. 

Brooks [II, ( L. Kirphis. M. Pcuill, B.M. Proteins A I heoreiiral Perspective of Dynamics, Struc.lure, and Phemiodynam ics, in Advances in Che.mioal Physios. Vol. 7 1. John Wiley iind Son s. New York, 1 9HS. 

Allhough more lhan 700 differenl ammo acids are known lo occur nalurally a group of 20 of Ihem commands special allenlion These 20 are Ihe ammo acids lhal are normally presenl m proteins and are listed m Table 27 1 All Ihe ammo acids from which proteins are derived are a ammo acids and all bul one of Ihese conlam a primary ammo funclion and conform lo Ihe general slruclure... 

Phenylalanine and tryptophan have side chains that incorporate aromatic rings which are large and hydrophobic The aromatic portion of tryptophan is bicyclic which makes it larger than phenylalanine Tryptophan also has a more electron rich aromatic ring and is more polarizable than phenylalanine Its role is more specialized and it is less abundant m proteins than most of the other ammo acids... 

A novel technique for dating archaeological samples called ammo acid racemiza tion (AAR) IS based on the stereochemistry of ammo acids Over time the configuration at the a carbon atom of a protein s ammo acids is lost m a reaction that follows first order kinetics When the a carbon is the only chirality center this process corresponds to racemization For an ammo acid with two chirality centers changing the configuration of the a carbon from L to D gives a diastereomer In the case of isoleucme for example the diastereomer is an ammo acid not normally present m proteins called alloisoleucme... 

Except for glycine which is achiral all of the a ammo acids present m proteins are chiral and have the l configuration at the a carbon... 

Section 28 11 Three RNAs are involved m gene expression In the transcription phase a strand of messenger RNA (mRNA) is synthesized from a DNA tern plate The four bases A G C and U taken three at a time generate 64 possible combinations called codons These 64 codons comprise the genetic code and code for the 20 ammo acids found m proteins plus start and stop signals The mRNA sequence is translated into a prescribed protein sequence at the ribosomes There small polynucleotides called... 

T Ichiye, M Karplus. Collective motions m proteins A covariance analysis of atomic fluctuations m molecular dynamics and normal mode simulations. Proteins Stiaict Eunct Genet 11 205-217, 1991. 

ANE Garcia. Large-amplitude nonlinear motions m proteins. Phys Rev Lett 68 2696-2699, 1992. 

SI O Donoghue, M Nilges. Calculation of symmetric oligomer stiaictures from NMR data. In R Krishna, IF Berliner, eds. Modern Techniques m Protein NMR, vol. 17 of Biological Magnetic Resonance. New York Kluwer Academic/Plenum, pp 131-161, 1999. 

DT Jones. Progress m protein stiaicture prediction. Curr Opin Stiaict Biol 7 377-387, 1997. 

BVB Reddy TL Blundell. Packing of secondary structural elements m proteins. Analysis and prediction of mter-helix distances. J Mol Biol 233 464-479, 1993. 

A Sail, TL Blundell. Definition of general topological equivalence m protein structures A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 212 403-428, 1990. 

WR Taylor, K Hatrick. Compensating changes m protein multiple sequence alignments. Protein Eng 7 341-348, 1994. 

J Moult, MNG James. An algorithm for determining the conformation of polypeptide segments m proteins by systematic search. Proteins 1 146-163, 1986. 

BL Sibanda, TL Blundell, JM Thornton. Conformation of (I-hairpms m protein stractures A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206 759-777, 1989. 

CS Ring, DG Kneller, R Langndge, FE Cohen. Taxonomy and conformational analysis of loops m proteins. I Mol Biol 224 685-699, 1992. 

D Rosenbach, R Rosenfeld. Simultaneous modeling of multiple loops m proteins. Protein Sci 4 496-505, 1995. 

P Koehl, M Delame. A self consistent mean field approach to simultaneous gap closure and side-chain positioning m protein homology modelling. Nature Struct Biol 2 163-170, 1995. R Samudrala, J Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279 287-302, 1998. 

RB Russell, GJ Barton. Structural features can be unconserved m proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J Mol Biol 244 332-350, 1994. 

MJE Sternberg, PA Bates, LA Kelley, RM MacCallum. Progress m protein structure prediction Assessment of CASP3. Curr Opm Struct Biol 9 368-373, 1999. 

C Bystroff, D Baker. Prediction of local structure m proteins using a library of sequence-structure motifs. J Mol Biol 281 565-577, 1998. 

G Baumann, C Frdmmel, C Sander. Polarity as a criterion m protein design. Protein Eng 2 239-334, 1989. 

SH Bryant, CE Lawrence. The frequency of lon-pair substructures m proteins is quantitatively related to electrostatic potential A statistical model for nonbonded interactions. Proteins 9 108-119, 1991. 

A Eiser, RKG Do, A Sail. Modeling of loops m protein structures. Prot Sci 9 1753-1773,... 

MT McMahon, E Oldfield. Determination of order parameters and correlation times m proteins A comparison between Bayesian, Monte Carlo and simple graphical methods. I Biomol NMR 13 133-137, 1999. 

J Janin, S Wodak, M Levitt, B Maigret. Conformations of ammo acid side-chains m proteins. J Mol Biol 125 357-386, 1978. 

N Go, H Taketomi. Respective roles of short- and long-range interactions m protein folding. Proc Natl Acad Sci USA 75 559-563, 1978. 

AK Churg, A Warshel. Control of the redox potential of cytochrome c and microscopic dielectric effects m proteins. Biochemistry 25 1675, 1986. 

ST Russell, A Warshel. Calculations of electrostatic energies m proteins The energetics of ionized groups m bovine pancreatic trypsin inhibitor. J Mol Biol 185 389-404, 1985. 

Perutz, M. Protein Structure New Approaches to Disease and Therapy. New York Freeman, 1992. 

Troponin C Troponin I Troponin T Minor M protein 18 21 31 165 2 M line Ca binding Inhibits actin-myosin interaction Binds to tropomyosin Binds to myosin... 

Organization into macromolecular structures. There are no apparent templates necessary for the assembly of muscle filaments. The association of the component proteins in vitro is spontaneous, stable, and relatively quick. Filaments will form in vitro from the myosins or actins from all three kinds of muscle. Yet in vitro smooth muscle myosin filaments are found to be stable only in solutions somewhat different from in vivo conditions. The organizing principles which govern the assembly of myosin filaments in smooth muscle are not well understood. It is clear, however, a filament is a sturdy structure and that individual myosin molecules go in and out of filaments whose structure remains in a functional steady-state. As described above, the crossbridges sticking out of one side of a smooth muscle myosin filament are all oriented and presumably all pull on the actin filament in one direction along the filament axis, while on the other side the crossbridges all point and pull in the opposite direction. The complement of minor proteins involved in the structure of the smooth muscle myosin filament is unknown, albeit not the same as that of skeletal muscle since C-protein and M-protein are absent. 

Fig. 1. Spectrum of potato calluses isoperoxidases (a) non-infected plants protein extract, (b) protein extract from plants, infected by P. infestans. M - protein markers.

Resistance to phagocytosis is sometimes associated with specific components of the cell wall and/or with the presence of capsules surrounding the cell wall. Classic examples of these are the M-proteins of the streptococci and the polysaccharide capsules of pneumococci. The acidic polysaccharide K-antigens of Escherichia coli and Sal typhi behave similarly, in that (i) they can mediate attachment to the intestinal epithelial cells, and (ii) they render phagocytosis more difficult. Generally, possession of an extracellular capsule will reduce the likelihood of phagocytosis. 

Chang, N. and Klibanov, A. M., Protein chromatography in neat organic solvents, Biotech. Bioeng., 39, 575, 1992. 

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