Folded stmctures

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

The sequence space of proteins is extremely dense. The number of possible protein sequences is 20. It is clear that even by the fastest combinatorial procedure only a very small fraction of such sequences could have been synthesized. Of course, not all of these sequences will encode protein stmctures which for functional purjDoses are constrained to have certain characteristics. A natural question that arises is how do viable protein stmctures emerge from the vast sea of sequence space The two physical features of folded stmctures are (l)in general native proteins are compact but not maximally so. (2) The dense interior of proteins is largely made up of hydrophobic residues and the hydrophilic residues are better accommodated on the surface. These characteristics give the folded stmctures a lower free energy in comparison to all other confonnations. 

The large molecule consists of a single peptide chain 35% P-sheet and 20% helical structure are found in the folded stmcture. The active site is a 1.2 nm deep conical cavity in the central pleated sheet, with a ion located at its bottom. Three histidine residues hold the Zn +, which also binds an HjO molecule. The active-site cavity is divided into hydrophilic and hydrophobic halves. The inhibitors of the enzyme replace the water on the Zn + ion and also block the fifth coordination site where COj should bind. 

For vimses that have an ssDNA or RNA genome, the exposed bases are capable of forming hydrogen bonds with complimentary bases that are in dose spatial proximity. Outside the viral capsid, these favorable base-pairing interactions lead to compact conformations, overcoming the entropic penalty of adopting folded stmctures that lack the conformational freedom of their rmfolded counterparts. Such interactions lead to a dramatic decrease in the size of the unconfined RNA... 

Figure 4 DNA-synthetic polymer conjugates, (a) Incorporating extended aromatic molecules into DNA creates folded stmctures through jT-stacking. (b) Block copolymers consisting of DNA and synthetic polymers can be assembled into micelles via microphase separation of incompatible blocks, (c) A PEG-DNA-brush block copolymer can shape shift between spherical and cylindrical micelles depending on the specific DNA input, (d) Dendritic DNA, created by covalently modifying short DNA strands with dendritic oligoethylene moieties, self-assembles into long-range fibers without the need for sticky-end cohesion.

Normal hydrocarbons with more than about 150 carbon atoms can also form folded stmctures under appropriate conditions. 

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