Structural Modifications of Proteins During Aging

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111120/1/j.1532-5415.1997.tb01518.x.pd

The Interdisciplinary Biophysics Graduate Program at the University of Michigan

The Michigan Biophysics Graduate Program (MBGP) was established in 1949, making it one of the first such programs in the world. The intellectual base of the program was significantly broadened in the 1980 when faculty members from a number of other units on campus were invited to join. Currently over forty faculty members from a variety of disciplines participate as mentors for the Ph.D. students enrolled in the MBGP providing our students with rich opportunities for academic learning and research. The MBGP has two main objectives: 1) to provide graduate students with both the intellectual and technical training in modern biophysics, 2) to sensitize our students to the power and unique opportunities of interdisciplinary work and thinking so as to train them to conduct research that crosses the boundaries between the biological and physical sciences. The program offers students opportunities to conduct research in a variety of areas of contemporary biophysics including structural biology, single molecule spectroscopy, spectroscopy and its applications, computational biology, membrane biophysics, neurobiophysics and enzymology. The MBGP offers a balanced curriculum that aims to provide our students with a strong academic base and, at the same time, accommodate their different academic backgrounds. Judging its past performance through the success of its former students, the MBGP has been highly successful, and there is every reason to believe that strong training in the biophysical sciences, as provided by the MBGP, will become even more valuable in the future both in the academic and the industrial settings. in the academic and the industrial settings. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 256–261, 2008.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58018/1/20931_ftp.pd

Age-related modifications in rat cardiac phosphoglycerate kinase. Rejuvenation of the old enzyme by unfolding-refolding

The occurrence of age-related modifications in functional and structural properties of several enzymes has been documented; however, the molecular basis of this phenomenon is still mostly unexplained. In the present work a comparative study of phosphoglycerate kinase preparations isolated from hearts of young and old rats was undertaken. Marked age-related effects wer revealed in the heat-inactivation kinetics of the enzyme, similar to the ones previously found in purified muscle phosphoglycerate kinase. In view of the previously reported failure of immunotitration to distinguish between phosphoglycerate kinase forms in crude heart extracts from young and old rats, it appears likely that the modifications in old rat heart phosphoglycerate kinase are in a domain which is not involved in antibody binding, and may be localized in the interior of the enzyme. These age-related modifications were completely relieved by extensive unfolding of the enzyme in 2 M guanidine hydrochloride, followed by enzyme reactivation upon dilution of the denaturant. The refolding products of young and old enzymes displayed identical heat-inactivation kinetics as native young phosphoglycerate kinase. It is concluded that the age-related alterations in rat cardiac phosphoglycerate kinase, like those found in the muscle enzyme, are purely conformational and hence develop postsynthetically.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27262/1/0000271.pd

Mechanism of aging of rat muscle glyceraldehyde-3-phosphate dehydrogenase studied by selective enzyme-oxidation

Controlled oxidation of rat muscle glyceraldehyde-3-phosphate dehydrogenase (GPDH) was carried out in an attempt to simulate age-related effects observed in enzyme samples purified from old animals. A comparative study of the "simulated aged" and of native young and old GPDH forms was done using fluorescence techniques. The present work is based on our previous findings that the locus of the age-related modifications in GPDH is in the nicotinamide-binding site, where the catalytically active Cys-149 residue is located, and that an increase in oxidation potential occurs in old animal tissues which may enable various oxidizing agents to play a significant role in the inactivation of certain enzymes. Thus it has been suggested that the loss of specific activity observed in old GPDH may be due to subtle and irreversible conformational changes caused by reaction of Cys-149 with these agents.The circularly polarized luminescence (CPL) spectrum emitted by the fluorescent sulfhydryl reagent I-AEDANS covalently bound to GPDH through Cys-149 at the nicotinamide binding site, revealed a significant difference in conformation between these sites in young and old GPDH forms. Large differences were also observed between corresponding spectra when the binding sites were saturated with NAD+, reflecting the development of marked conformational changes in both young and old GPDH species upon coenzyme binding.The oxidizing reagents employed in the current study (hydrogen peroxide, superoxide radical and atmospheric dioxygen) are all expected to be more commonly encountered in the less reducing environment of old animal tissues. All of them, though to a different extent, caused a significant inactivation of the enzyme dependent on the initial oxidant concentration. Although the original enzymatic activity could be partially restored by incubation with a reducing agent, the prior oxidation was found to induce some irreversible structural changes as expressed in a decrease in the number of fast reacting SH groups. The extent of irreversible inactivation was a function of both oxidant concentration and the duration of exposure to the oxidant.The affinity of the oxidized GPDH species (termed "aged") toward coenzyme, as monitored by fluorometric titrations, was markedly lower than that observed for both the native young and old GPDHs. In addition, the CPL spectra of the "aged" enzymes were different from those obtained for both native forms. This indicates that the structural modifications induced by the oxidation reactions tested differ from those present in native old GPDH, although in each case the changes are localized within the nicotinamide binding site.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26555/1/0000094.pd

A comparative study of succinate-supported respiration and ATP/ADP translocation in liver mitochondria from adult and old rats

This study was undertaken to compare the rates of succinate-supported hepatic mitochondrial respiration between 12 months (adult) and 29 months (old) male Fischer 344 rats. Experiments were also performed to determine the activity of adenine nucleotide translocase and the effect of its inhibition on mitochondrial respiration. Succinate-supported state 3 mitochondrial respiration was found to decline 20% between 12 and 29 months of age in rat liver, along with a similar 25% decrease in the respiratory control ratio with age. Adenine nucleotide translocase activity is shown to decrease 39% from adult to old rat liver mitochondria. This decrease does not, however, account for the decline in state 3 respiration, since translocase activity is approximately 50% greater than state 3 respiration in both adult and old rats. Therefore, adenine nucleotide translocase is not rate-limiting for state 3 mitochondrial respiration.Neither the rate of succinate permeation into the mitochondrion nor the rate of electron transport is rate-limiting for state 3 respiration, indicated by the greatly increased oxygen consumption with addition of the uncoupler carbonyl cyanide m-chlorophenyl hydrazone (m-CCCP). These processes, therefore, are not responsible for the observed decline in state 3 respiration. The implications and possible cause of the age-related decrease in the maximal rate of ATP-synthesis are discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29281/1/0000340.pd

Renaturation of glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides after denaturation in 4 M guanidine hydrochloride: kinetics of aggregation and reactivation

In 4 M guanidine hydrochloride (GdnHCl), the dimeric enzyme glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides (G6PD) dissociated to subunits and was extensively unfolded. Rapid dilution of this high GdnHCl concentration allowed G6PD to partially renature, as measured by enzyme reactivation, to a level which depended on the conditions employed. The fraction of the enzyme which did not renature aggregated and precipitated out of solution, a process which could not be substantially prevented by stabilizing additives. Based on the enzyme concentration dependence of the reactivation yield and on a comparison of the aggregation and reactivation rates, it was determined that aggregation and reactivation compete kinetically for a partially-folded intermediate only very early in the process, during the rapid GdnHCl-dilution step. The kinetics of G6PD reactivation were sigmoidal, indicating that this process involves more than one rate-limiting reaction. The kinetics depended on enzyme concentration in a higher than first-order manner, indicating that association of subunits is one of the rate-limiting reactions. A renaturation mechanism compatible with these observations is described, which involves a bi-unimolecular (subunit association-folding) reaction sequence, with rate constants equal to 2.19 [mu]M-1 min-1 and 0.140 min-1, respectively. This mechanism involves an inactive, dimeric, G6PD-folding intermediate, a species whose existance has recently been established by equilibrium denaturation experiments (Plomer, J.J. and Gafni, A. (1992) Biochim. Biophys. Acta 1122, 234-242).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30836/1/0000498.pd

Denaturation of glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides by guanidine hydrochloride; identification of inactive, partially unfolded, dimeric intermediates

The denaturation of the dimeric enzyme glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides by guanidine hydrochloride has been studied using enzymatic activity, intrinsic fluorescence, circular dichroism, and light scattering measurements. Equilibrium experiments at 25[deg]C revealed that between 0.9 and 1.2 m denaturant the enzyme underwent a conformational change, exposing tryptophan residues to solvent, with some loss of secondary structure and a complete loss of enzymatic activity but without dimer dissociation to subunits. This inactive, partially unfolded, dimeric intermediate was susceptible to slow aggregation, perhaps due to exposure of `sticky' hydrophobic stretches of the polypeptide chain. A second equilibrium transition, reflecting extensive unfolding and dimer dissociation, occurred only at denaturant concentrations above 1.4 M. Kinetics experiments demonstrated that in the denaturant concentration range of 1.7-1.9 M the fluorescence change occurred in two distinct steps. The first step involved a large, very rapid drop in fluorescence whose rate was strongly dependent on the denaturant concentration. This was followed by a small, relatively slow rise in the emission intensity, the rate of which was independent of denaturant concentration. Enzymatic activity was lost with a denaturant-concentration-dependent rate, which was approx. 3-times slower than the rate of the first step in fluorescence change. A denaturation mechanism incorporating several unfolding intermediates and which accounts for all the above results is presented and discussed. While the fully unfolded enzyme regained up to 55% of its original activity upon dilution of denaturant to a concentration that would be expected to support native enzyme, denaturation intermediates were able to reactivate only minimally and in fact were found to aggregate and precipitate out of solution.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29896/1/0000253.pd

Single-Molecule Imaging Reveals Aβ42:Aβ40 Ratio-Dependent Oligomer Growth on Neuronal Processes

AbstractSoluble oligomers of the amyloid-β peptide have been implicated as proximal neurotoxins in Alzheimer’s disease. However, the identity of the neurotoxic aggregate(s) and the mechanisms by which these species induce neuronal dysfunction remain uncertain. Physiologically relevant experimentation is hindered by the low endogenous concentrations of the peptide, the metastability of Aβ oligomers, and the wide range of observed interactions between Aβ and biological membranes. Single-molecule microscopy represents one avenue for overcoming these challenges. Using this technique, we find that Aβ binds to primary rat hippocampal neurons at physiological concentrations. Although amyloid-β(1–40) as well as amyloid-β(1–42) initially form larger oligomers on neurites than on glass slides, a 1:1 mix of the two peptides result in smaller neurite-bound oligomers than those detected on-slide or for either peptide alone. With 1 nM peptide in solution, Aβ40 oligomers do not grow over the course of 48 h, Aβ42 oligomers grow slightly, and oligomers of a 1:1 mix grow substantially. Evidently, small Aβ oligomers are capable of binding to neurons at physiological concentrations and grow at rates dependent on local Aβ42:Aβ40 ratios. These results are intriguing in light of the increased Aβ42:Aβ40 ratios shown to correlate with familial Alzheimer’s disease mutations

Lack of correspondence between the room-temperature phosphorescence decay-components and Trp residues in a series of Trp-->Cys or Trp-->Phemutants of human carbonic anhydrase II

The room temperature phosphorescence of native human carbonic anhydrase (CA), and several mutants of this enzyme has been investigated. In these mutants the seven tryptophan residues in the native protein have sequentially been replaced by cysteine or phenylalanine. All of the mutants as well as native CA show room-temperature tryptophan phosphorescence (RTP) spectra. Surprisingly, only small differences in RTP life-times are noticeable among these mutants, indicating that there is more than one tryptophan residue with similar phosphorescence decay kinetics in the protein. The present results illustrate the danger in attributing the room temperature phosphorescence of a multi-tryptophan protein to a particular residue based solely on an analysis of the protein structure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31251/1/0000157.pd

Direct Observation of Single Amyloid-β(1-40) Oligomers on Live Cells: Binding and Growth at Physiological Concentrations

Understanding how amyloid-β peptide interacts with living cells on a molecular level is critical to development of targeted treatments for Alzheimer's disease. Evidence that oligomeric Aβ interacts with neuronal cell membranes has been provided, but the mechanism by which membrane binding occurs and the exact stoichiometry of the neurotoxic aggregates remain elusive. Physiologically relevant experimentation is hindered by the high Aβ concentrations required for most biochemical analyses, the metastable nature of Aβ aggregates, and the complex variety of Aβ species present under physiological conditions. Here we use single molecule microscopy to overcome these challenges, presenting direct optical evidence that small Aβ(1-40) oligomers bind to living neuroblastoma cells at physiological Aβ concentrations. Single particle fluorescence intensity measurements indicate that cell-bound Aβ species range in size from monomers to hexamers and greater, with the majority of bound oligomers falling in the dimer-to-tetramer range. Furthermore, while low-molecular weight oligomeric species do form in solution, the membrane-bound oligomer size distribution is shifted towards larger aggregates, indicating either that bound Aβ oligomers can rapidly increase in size or that these oligomers cluster at specific sites on the membrane. Calcium indicator studies demonstrate that small oligomer binding at physiological concentrations induces only mild, sporadic calcium leakage. These findings support the hypothesis that small oligomers are the primary Aβ species that interact with neurons at physiological concentrations