Protein nucleation

Effect of UV Light on Amyloidogenic Proteins Nucleation and Fibril Extension... 

Many lines of evidence suggest that molecular preassociation may be important for protein nucleation and growth. 

Nucleation of protein crystals typically requires extremely high supersaturation levels. Studies of protein nucleation are limited, with most efforts focused on light scattering as a tool to detect nucleation. Feher and Kam s work set the tone for much of the work that followed (Feher and Kam 1985). They model nucleation in a classical fashion, as a cooperative step-by-step addition of monomers to a cluster. Light scattering is utilized to follow the cluster size distribution as a function of time and solution variables, which yield estimates for the relative forward (cluster growth) and reverse (cluster dissolution) rates of monomer addition. Certainly, the protein crystal nucleation is an area that deserves additional study. 

Figure 12.18 The ideal trajectory of a vapor diffusion experiment. The arrow indicates the composition changes that might take place in the evaporating droplet with a simultaneous protein nucleation and growth.

Monomer-Binding Proteins Nucleation, Monomer Sequestration, and Nucleotide Exchange 189... 

Curcio, E., Curcio, V., Di Rrofio, G., Fontananova, E. and Drioli, E. 2010. Energetics of protein nucleation on rough polymeric surfaces, 114 13650-13655. 

Stolyarova, S., Baskin, E., Chayen, N.E. and Nemirovsky, Y. 2005. Possible model of protein nucleation and crystallization on porous silicon. 8 1462-1466. 

Guo Z and Thirumalai D 1995 Kinetics of protein folding nucleation mechanism, time scales and pathways Biopolymers 36 83-103... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

A continuous lipidic cubic phase is obtained by mixing a long-chain lipid such as monoolein with a small amount of water. The result is a highly viscous state where the lipids are packed in curved continuous bilayers extending in three dimensions and which are interpenetrated by communicating aqueous channels. Crystallization of incorporated proteins starts inside the lipid phase and growth is achieved by lateral diffusion of the protein molecules to the nucleation sites. This system has recently been used to obtain three-dimensional crystals 20 x 20 x 8 pm in size of the membrane protein bacteriorhodopsin, which diffracted to 2 A resolution using a microfocus beam at the European Synchrotron Radiation Facility. 

A. M. Kierzek, W. M. Wolf, P. Zielenkiewicz. Simulations of nucleation and early growth stages of protein crystals. Biophys J 75 571, 1997. 

Centrosomes, also called the microtubule organizing centre, are protein complexes that contain two cen-trioles (ringlike structures) and y- tubulin. They serve as nucleation points for microtubular polymerization and constrain the lattice structure of a microtubule to 13 protofilaments. They are responsible for organizing the mitotic spindle during mitosis. 

MT-associated proteins (MAPs) are attached to MTs in vivo and play a role in their nucleation, growth, shrinkage, stabilization and motion. Of the MAPs, the tau family proteins have received special attention as they are involved in the pathophysiology of Alzheimer s disease. 

The microtubule-associated proteins MAP2 and tau both have two separate functional regions (Lewis et al., 1989). One is the microtubule-binding site, which nucleates microtubule assembly and controls the rate of elongation (by slowing the rate of assembly). The second functional domain shared by MAP2 and tau is a short C-terminal a-helical sequence that can cross-link microtubules into bundles by self-interaction. This domain has some of the properties of a leucine zipper. Likely it is responsible for the organization of microtubules into dense stable parallel arrays in axons and dendrites (Lewis et al., 1989). 

In the first step, lipid model membranes have been generated (Fig. 15) on the air/liquid interface, on a glass micropipette (see Section VIII.A.1), and on an aperture that separates two cells filled with subphase (see Section VIII.A.2). Further, amphiphilic lipid molecules have been self-assembled in an aqueous medium surrounding unilamellar vesicles (see Section VIII.A.3). Subsequently, the S-layer protein of B. coagulans E38/vl, B. stearother-mophilus PV72/p2, or B. sphaericus CCM 2177 have been injected into the aqueous subphase (Fig. 15). As on solid supports, crystal growth of S-layer lattices on planar or vesicular lipid films is initiated simultaneously at many randomly distributed nucleation... 

Rephcation errors, even with a very efficient repair system, lead to the accumulation of mutations. A human has 10 nucleated cells each with 3 X 10 base pairs of DNA. If about 10 cell divisions occur in a lifetime and 10 mutations per base pair per cell generation escape repair, there may evenmaUy be as many as one mutation per 10 bp in the genome. Formnately, most of these will probably occur in DNA that does not encode proteins or will not affect the function of encoded proteins and so are of no consequence. In addition, spontaneous and chemically induced damage to DNA must be repaired. 

The nucleat receptor superfamily of proteins plays a centtal tole in the regulation of gene transcription. 

These macromolecules include histones, ribosomal proteins and ribosomal subunits, ttansctiption factors, and mRNA molecules. The transport is bidirectional and occurs through the nucleat pote complexes (NPCs). These are complex stmctures with a mass approximately 30 times that of a ribosome and are composed of about 100 diffetent proteins. The diameter of an NPC is approximately 9 run but can increase up to ap-ptoximately 28 nm. Molecules smaller than about 40 kDa can pass through the channel of the NPC by diffusion, but special translocation mechanisms exist fot latget molecules. These mechanisms are under intensive investigation, but some important features have already emerged. 

Recent interest has focused on acidic phosphoproteins, such as bone sialoprotein, acting as sites of nucleation. These proteins contain motifs (eg, poly-Asp and poly-Glu stretches) that bind calcium and may provide an initial scaffold for mineralization. Some macromolecules, such as certain proteoglycans and glycoproteins, can also act as inhibitors of nucleation. 

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