Determination of protein secondary structure by Fourier transform infrared spectroscopy: A critical assessment

Abstract

The ultimate goal of structural studies of proteins is to gain insight into protein three-dimensional structure at highresolution level. This can often be accomplished by the application of techniques such as X-ray crystallography or multidimensional nuclear magnetic resonance (NMR) spectroscopy. However, high-resolution studies of proteins are not always feasible. For example, crystallographic studies require high-quality single crystals which for many proteins (e.g., the vast majority of membrane proteins) are not available. Furthermore, the question arises as to whether the relatively "static" structure in single crystals adequately represents the protein conformation in a complex and dynamic environment of living cells. There is a growing realization [e.g., Martinek et al. (1989)] that in vivo most proteins act in an interfacial environment where they form dynamic complexes with biological membranes, nucleic acids, polysaccharides, or other proteins. Aqueous buffers, from which protein crystals are usually grown, do not necessarily mimic well the conditions of protein functioning in vivo. NMR offers a somewhat better flexibility in studying protein structure in "biologically relevant" environments. However, the interpretation of NMR spectra of larger proteins is very complex, and the assignment of interproton distances generated by the NMR experiment is not always feasible; at present the technique is restricted to small proteins of less than approximately 15-20 kDa.The practical limitations encountered in high-resolution structural studies of proteins stimulate continual progress in f This is National Research Council of Canada Publication No. NRCC 34263.

Time-Course and Regional Analyses of the Physiopathological Changes Induced after Cerebral Injection of an Amyloid β Fragment in Rats

“…4 Structure-activity studies revealed that peptides containing the highly hydrophobic 25-35 region formed stable aggregates and mediated neuronal death by necrosis or apoptosis. 5,6,7 The truncated A␤ [25][26][27][28][29][30][31][32][33][34][35] fragment includes extracellular and intramembrane residues that have been reported to represent an active region of A␤. 8 In vivo, two nontransgenic rodent models of AD have been studied to analyze the molecular, morphological, and behavioral consequences of amyloid toxicity: the infusion of A␤ 1-40/42 protein and the injection of preaggregated A␤ [25][26][27][28][29][30][31][32][33][34][35] peptide.…”

“…These models have led to highly pertinent pathomimetic observations and provide complementary approaches to the numerous transgenic mouse lines developed as AD models. In particular, at 1 week after A␤ [25][26][27][28][29][30][31][32][33][34][35] injection, reactive gliosis was observed in the rat hippocampus, 9 caspase-3 activity was induced in the hippocampus and cortex, 9 a reduction in the number of neurons was measured in the CA1 or CA3 hippocampal area, 9 -11 and significant oxidative stress was observed. [11][12][13] Nonetheless, this amyloid toxicity model remains controversial with respect to AD.…”

“…First, although the presence of A␤ [25][26][27][28][29][30][31][32][33][34][35] has been repeatedly demonstrated in brains of AD patients, 14,15 this fragment appears to be a minor peptide in plaques and its contribution to the toxicity induced by all amyloid-related species remains unclear. Second, the intracerebroventricular injection of A␤ [25][26][27][28][29][30][31][32][33][34][35] induces marked toxicity within days or weeks, which is not in accord with the long-term progression of AD in humans (an argument that is unrelated to the nature of the toxicity). Third, it is possible that peptide injection mimics only the amyloid toxicity observed in AD physiopathology, but not the processes involved in A␤ formation or Tau protein hyperphosphorylation.…”

“…Klementiev et al 16 recently documented some evidence that contradicts this latter reservation. Moreover, very recently, Chavant et al 17 reported that, at 2 weeks after injection, A␤ [25][26][27][28][29][30][31][32][33][34][35] significantly increased APP processing in the hippocampus of mice.…”

“…We therefore analyzed the consequences of intracerebroventricular injection of aggregated A␤ [25][26][27][28][29][30][31][32][33][34][35] in terms of time-course changes and in different brain structures through several morphological, hormonal, biochemical, and behavioral parameters, as well as addressing the modifications in central APP processing, brain-derived neurotrophic factor (BDNF) levels, cerebral inflammation, and hippocampus vulnerability. We also evaluated over time the distribution within brain structures of the injected A␤ [25][26][27][28][29][30][31][32][33][34][35] fragment.…”