Rotamers model

This rotamer model for the fluorescence decay of an aromatic amino acid also predicts that the amplitudes of the kinetic components should correspond to the ground-state rotamer populations, provided that interconversion... 

Most studies use this three-state staggered rotamer model to analyze the coupling constants and thus to deduce the rotamer distribution, but other treatments of J couplings have also been described.102-104... 

J. Mendes, A. M. Baptista, M. A. Carrondo, C. M. Soares. Improved modeling of side-chains in proteins with rotamer-based methods a flexible rotamer model. Proteins. 1999, 37, 530-543. 

Finally, the rotamers model was introduced to explain the biexponential decay of the tryptophan in solution. If we have to apply tlie rotamers model to tryptophan in polypeptides, what will be the contribution of the protein structure and dynamics to the fluorescence lifetime ... 

In this example, it is difficult to assign a specific fluorescence lifetime to a specific Trp residue. Also, the rotamers model can in no way explain the origin of the fluorescence lifetimes. One can consider the fluorescence lifetime as being the result of the Trp residues interaction witli their microenvironments. However, since fluorescence lifetimes do not vary significantly witli die different mutants, one should consider the possibility of having, around the Trp residues, a common identical protein structure responsible of the three measured fluorescence lifetimes. 

Fluorescence intensity decay of the Trp residues ( ex, 300 nm) yields four fluorescence lifetimes, 0.22, 0.44, 2.06 and 4.46 ns. The authors considered the two shortest lifetimes as the result of the excited state quenching of the tryptophan emission by the protein backbone, while the two longest lifetimes are characteristics of the emission of the Trp residues from two different environments (Kung et al. 1998). Tryptophan free in solution emits with two lifetimes, 0.5 and 3.1 ns. In this case, the short lifetime cannot be assigned to the presence of a backbone protein. The two lifetimes are considered to be the result of the different side chain retainers conformations. Thus, a tryptophan in presence of different environments, water and protein matrix, can have the same or identical fluorescence lifetimes. This example shows clearly that it is not obvious to explain the origin of the fluorescence lifetime of tryptophan residues in proteins by the rotamers model. 

Nevertheless, let us discuss now the HIV -1 protease fluorescence in terms of rotamers model. The purpose of this discussion is to find out how far we can go in the application of this model. Therefore, let us consider the rotamers model as correct and thus the two fluorescence lifetimes (0.5 and 3.1 ns) of free Trp in solution originates from two rotamers. If this model is correct in proteins also and thus in HIV-1 protease, we have two tryptophans with four lifetimes, two short (close to 0.5 ns) and two long (close to 3.1 ns). Thus, we can attribute to each tryptophan, long and short fluorescence lifetimes. In other terms, the presence of the protein matrix around Trp residues does not play any fundamental role in the fluorescence lifetimes of the Trp residues. In this case, the protein backbone has no effect or non significant effect on the fluorescence lifetime of HIV-1 protease. In simple words, the fluorescence lifetime of tryptophan would be in dependent of the tertiary structure of HIV-1 protease. 

Fluorescence emission lifetime of one tryptophan residue located in five different positions within an 18-residue amphiphatic peptide (Table 7.5) was also analyzed with the rotamers model. These peptides are unstructured in aqueous solution and become stmctured when associated to a lipid. A blue shift in the emission maximum of the Trp residue is observed, indicating that the fluorophore is in contact with a hydrophobic environment when the lipid is bound to the peptides. Only peptide 18D-12 shows an emission maximum located at 354 revealing that in this peptide tryptophan is in contact with aqueous environment. These data are consistent witli the fact that association of lipid with peptide yield an a-helix where the tryptophan residues located on the hydrophobic surface of the a-helix are in the hydrophobic environment provided by the lipid surface, whereas tryptophans located on the hydrophilic face of the helix are directed toward the aqueous phase. Also, the helix axis of the peptides is parallel to the lipid surface (Fig. 7.9). 

In the present two cases, the results described in Table 7.9 indicate that the rotamers model is not adequate to describe the origin of the fluorescence lifetime of the tryptophans in the two proteins. The shortest fluorescence lifetime (35 or 45 ps) found also for tryptophan residues in myoglobin is an indication of the high energy transfer Forster type from tryptophans to heme. We believe that this lifetime is common or almost all hemoproteins where energy transfer between tryptophan(s) and the heme is very important. 

When motion effects are expected to be due to the existence ofdifierent conformations (multiple rotameric states significantly populated), rather to local fluctuations, they can also be accounted for with staggered-rotamer models [29], in which discrete probabilities for the different conformers are introduced. They are often used when describing amino acid side-chain torsion conformations. See, for instance. Ref [30] for a recent critical analysis of several models. 

MJ Bower, FE Cohen, RL Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library A new homology modeling tool. J Mol Biol 267 1268-1282, 1997. 

C Wilson, LM Gregoret, DA Agard. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search. J Mol Biol 229 996-1006, 1993. 

Certain side-chain conformations are energetically mote favorable than others. Computer programs used to model protein structures contain rotamer libraries of such favored conformations. 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Fig. 1. Rotational profile for l,r,3,3 -tetrakis(trimethylsilyl)ferrocene 78, as deduced from simple molecular model consideration. For the designation of the various rotamers see text...

Adducts of M(CH-f-Bu)(NAr)(OR)2 complexes were prepared and studied as models for the initial olefin adduct [66] in an olefin metathesis reaction [67]. PMe3 was found to attack the CNO face of yy -M(CH-f-Bu)(NAr)(OR)2 rotamers to give TBP species in which the phosphine is bound in an axial position... 

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