Macromolecular interactions

Pommier, Y., and Cherfils, J. (2005). Interfacial inhibition of macromolecular interactions Nature s paradigm for drag discovery. Trend. Pharmacol. Sci. 26 138—145. 

Stott WT, Quast JF, Watanabe PG. 1982. Pharmacokinetics and macromolecular interactions of trichloroethylene in mice and rats. Toxicol Appl Pharmacol 62 137-151. 

Morton, T. A., and Myszka, D. G. (1998). Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors. Methods Enzymol. 295, 268-294. 

Ackers, G. (1998), Deciphering the molecular code of hemoglobin allostery , in Di Cera (Ed ), Advances in Protein Chemistry, Vol. 51, Linkage Thermodynamics of Macromolecular Interactions, Academic Press, San Diego, CA, pp. 185-253... 

The number of commercially available crosslinkers for sulfhydryl and photoreactive conjugations provides enough variety to design successful experiments in photolabeling, such as studying active centers and macromolecular interactions. 

The introduction of optical biosensors has made it possible to obtain data for a large number of macromolecular interactions without the necessity of additional labeling. Here several commercial instruments utilize the effect of Surface Plasmon Resonance (SPR) to detect accumulation of ligands in the sensor matrix. 

Pommier Y, Cherfils J. (2005) Interfacial inhibition of macromolecular interactions Natnre s paradigm for dmg discovery. Trends Pharmacol Sci 26 138-145. 

Application to Macromolecular Interactions. Chun describes how one can analyze the thermodynamics of a particular biological system as well as the thermal transition taking place. Briefly, it is necessary to extrapolate thermodynamic parameters over a broad temperature range. Enthalpy, entropy, and heat capacity terms are evaluated as partial derivatives of the Gibbs free energy function defined by Helmholtz-Kelvin s expression, assuming that the heat capacities integral is a continuous function. 

Reayi A, Arya P. (2005) Natural product-like chemical space Search for chemical dissectors of macromolecular interactions. Curr. Opin. Chem. Biol. 9 240-247. 

Elwing H, WeUn S, Askendal A, Nilsson U, LundstiOm I (1987) A wettabihty gradient method for studies of macromolecular interactions at the Uquid/solid interface. J Colloid Interface Sci 119 203-210... 

Semenova, M.G. (1996). Factors determining the character of biopolymer-biopolymer interactions in multicomponent aqueous solutions modelling food systems. In Parris, N., Kato, A., Creamer, L.K., Pearce, J. (Eds). Macromolecular Interactions in Food Technology, ACS Symposium Series No. 650, Washington, D.C. American Chemical Society, pp. 37 19. 

Reitz, R.H., Fox, T.R., Ramsey, J.C., Quast, J.F., Langvardt, PW. Watanabe, P.G. (1982) Pharmacokinetics and macromolecular interactions of ethylene dichloride in rats after inhalation or gavage. Toxicol, appl. Pharmacol., 62, 190-204... 

O. G. Berg and P. H. Vonhippel, Diffusion-controlled macromolecular interactions, Annu. Rev. Biophys. Biophys. Chem. 14, 131-160 (1985). 

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and /J-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

Since the compatibility of macromolecules is extensively discussed in many works on the -parameter18, it is treated here only briefly. When considering the compatibility of polymers, one must naturally give thought to weak inter-macromolecular interactions, for example, van der Waals force, dipole-dipole interaction, and so on. 

It is likely that protein binding and other macromolecular interactions also play a role in stabilizing the rRNA structures. A recent analysis12 reveals that the binding of specific ribosomal protein to rRNA in vitro results in changes within the rRNA modification patterns. Because the experiments detailed herein examine a population of rRNA within the cell, and thus may be analyzing a variety of RNA conformations, it is remarkable that very consistent results are observed. However, the consequence of polysome assembly and translation on the structure of the rRNA and how these structures might be distinct are not addressed in this analysis. In vitro DMS modification of soybean RNA has revealed some differences in base reactivity relative to that observed on RNA modified in vivo as described herein.36 ... 

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