Self-Assembly of Synthetic and Biological Polymeric Systems of ...

5.2.1.- Unfolded state
Over the last decade, an enormous progress has been made in the description of the
conformation of the unfolded states of polypeptide chains. These important species not only
define the starting point for protein folding, but also have important roles in a variety of
biological process. When described the unfolded state of a polypeptide sequence, the first idea
in mind is a random coil structure, which lacks of specific inter-residue interactions between
the lateral chains of the amino acid sequence. However, this viewpoint has moved over recent
years as a result of the increasing number of detailed studies about the properties and
structure of denatured states under different solution conditions (98). Current views consider
that even in the presence of high denaturant concentrations, significant amounts of aliphatic
and aromatic side chains present in the native state may persist, even when the secondary
structure of the native state has been lost. On the other hand, under lesser harsh solution
conditions, also some proteins can be unfolded in the absence of denaturant agents (for
example, by mutating the sequence or changing the pH of the solution), the unfolded state has
been shown to contain significant native-like interactions with substantial native and non-
native side chain contacts which allow the existence of a residual structure. This residual
structure in the unfolded state has not only been suggested to reduce the conformational
search during protein folding, but also for some proteins may play a role in the onset of
protein aggregation of unfolded polypeptide sequences (97)(99).
5.2.2.- Intermediate and transition state ensembles
The function of the intermediate states (populated partially-folded states) during protein
folding has been a long-standing question. Supported by the observation that many small
proteins fold with apparent two-state kinetics, folding intermediates were initially thought to
be aberrant misfolds on the folding energy landscape, representing off-pathway species or
kinetics traps. Nowadays, thanks to more powerful experimental methods (Foster resonance
emission transfer fluorescence (FRET), fluorescent correlation spectroscopy or NMR
spectroscopy, amongst others) protein folding studies have revealed that partially folded
states are widely populated during the protein folding process, even in simplest proteins (97).
In this regard, a model that involves transient intermediate states in equilibrium into the
pathway of a given polypeptide chain has been suggested. Under this context, a polypeptide
chain with high molecular weight may present many intermediate states, describing a
roughness energy landscape for its particular folding pathway. For example, larger polypeptide
chains have a higher tendency to collapse under specific solution conditions, leading to the
formation of compact states, which can contain substantial native-like structure. Structural
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