NMR structures of thioredoxin m from the green alga Chlamydomonas reinhardtii

Chloroplast thioredoxin m from the green alga Chlamydomomas reinhardtii is very efficiently reduced in vitro and in vivo in the presence of photoreduced ferredoxin and a ferredoxin dependent ferredoxin-thioredoxin reductase. Once reduced, thioredoxin m has the capability to quickly activate the NADP malate dehydrogenase (EC 1.1.1.82) a regulatory enzyme involved in an energy-dependent assimilation of carbon dioxide in C4 plants. This activation is the result of the reduction of two disulfide bridges by thioredoxin m, that are located at the N- and C-terminii of the NADP malate dehydrogenase. The molecular structure of thioredoxin m was solved using NMR and compared to other known thioredoxins. Thioredoxin m belongs to the prokaryotic type of thioredoxin, which is divergent from the eukaryotic-type thioredoxins also represented in plants by the h (cytosolic) and f (chloroplastic) types of thioredoxins. The dynamics of the molecule have been assessed using (15)N relaxation data and are found to correlate well with regions of disorder found in the calculated NMR ensemble. The results obtained provide a novel basis to interpret the thioredoxin dependence of the activation of chloroplast NADP-malate dehydrogenase. The specific catalytic mechanism that takes place in the active site of thioredoxins is also discussed on the basis of the recent new understanding and especially in the light of the dual general acid-base catalysis exerted on the two cysteines of the redox active site. It is proposed that the two cysteines of the redox active site may insulate each other from solvent attack by specific packing of invariable hydrophobic amino acids.     

Protein–ligand structure guided by backbone and side-chain proton chemical shift perturbations

The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) –5 mM). The determination of the protein–fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for the protein–ligand recognition, and for growing the initial fragment into potent active compounds. The vast majority of fragments are aromatic compounds that induce chemical shift perturbations (CSP) on protein NMR spectra. These experimental CSPs can be quantitatively used to guide the ligand docking, through the comparison between experimental CSPs and CSP back-calculation based on the ring current effect. Here we implemented the CSP back-calculation into the scoring function of the program PLANTS. We compare the results obtained with CSPs measured either on amide or aliphatic protons of the human peroxiredoxin 5. We show that the different kinds of protons lead to different results for resolving the 3D structures of protein–fragment complexes, with the best results obtained with the \(\hbox {H}_{\alpha }\) protons.     

Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5

Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed ¹⁵N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.     

A moment-by-moment comparsion of sucrose and saccharin drinking by the rat

Comparisons were made between the ingestion patterns in ratsto a 0.2% sodium saccharin solution and to a 32% sucrose solutionin both short-term (30 min, one solution only) and long-term(23 h, solution versus water) tests. The resolution of measurementin the short- and long-term tests was 0.5 and 30 s respectively.Analysis programs for both procedures allowed for a quantificationof the ingestion patterns over time, showing details of thelick bursts in the short-term tests and ingestion bouts in the23-h tests. Although the quantities of sucrose and saccharinconsumed in the long-term tests were equal, the drinking patternsfor water, saccharin and sucrose were markedly different duringthe three testing periods, (i) There were fewer drinking boutsto the sucrose than to the saccharin or water, (ii) The averagebout of sucrose was much larger than the saccharin or waterbouts, (iii) The inter-bout intervals for sucrose were muchlonger than those for saccharin, (iv) Nearly half of the sucroseintake occurred during the ‘lights-on’ portion ofthe 23-h drinking period as compared to less than one-thirdfor saccharin or water, (v) Food intake when saccharin was presentwas equal to normal food intake when only water was available.However, in the presence of sucrose, the number and the sizeof feeding bouts decreased resulting in a 36% reduction in foodintake. Similar results were found in the short-term tests whencomparing sucrose and saccharin ingestion in that the quantitiesconsumed were not reliably different, but the ingestion patternswere, (i) The rats had many more bursts of licking saccharinthan sucrose, (ii) The saccharin bursts were much shorter thanthose for sucrose, (iii) Saccharin licking occurred off andon throughout the 30-min testing period while sucrose was consumedat a rapid rate at first and then terminated in 10–15min from the period onset. Inferences about the different tastesof saccharin and sucrose to the rat arc drawn from the detailedpattern analyses.     

Vibrational analysis of peptides, polypeptides, and proteins. XVII. Normal modes of crystalline Pro-Leu-Gly-NH2, a type II beta-turn

A normal mode calculation has been done for Pro-Leu-Gly-NH2 in its crystalline type II beta-turn structure, and assignments have been made to infrared and Raman bands of this molecule and its N-deuterated derivative. Observed and calculated frequencies below 1700 cm-1 agree to within about 6 cm-1. This analysis provides a sound basis for studying the conformation dependence of the vibrational spectrum.     

Circular dichroism of the “random” polypeptide chain

The circular dichroism (CD) spectrum of an unordered polypeptide chain does not correspond, as has been assumed heretofore, to that of a charged chain such as poly-L -glutamic acid or poly-L -lysine. The latter have been shown to have locally ordered structures with characteristic CD spectra. We have now obtained CD spectra of the unordered forms of the above synthetic, polypeptides, as well as of two fibrous proteins (collagen and feather keratin) and a globular protein (myoglobin). These spectra are all similar to that of unordered polyproline, having a negative band in the vicinity of 2000 mμ and no additional bands at longer wavelengths. The lack of structural uniqueness of the unordered polypeptide chain is emphasized by these studies.     

Studies on the Structure of Feather Keratin: II. A β-Helix Model for the Structure of Feather Keratin

The assumption that the proline residues in feather keratin, which comprise 12 per cent of the total, are periodically located along the polypeptide chain is shown to lead to an essentially unique structure for this fibrous protein. The structure is based on a β-helix; i.e., an extended chain which coils slowly to form a helix of relatively large pitch. Such helices tend to aggregate by hydrogen bonding to form cylindrical units, which in turn can aggregate further into cable-like structures. This model has been tested with respect to its predictions concerning the x-ray diffraction pattern, infrared spectrum, mechanical properties, and chemical behavior of feather keratin. Preliminary results indicate that it is better capable of accounting for the data than previously proposed structures.     

An infrared study of unordered poly-L-proline in CaCl 2 solutions

Infrared spectra have been obtained of poly-L -proline in aqueous CaCl₂ solutions. As the salt concentration is increased, the C?O stretching band develops a component at the frequency found in the solid state while the CH₂ bending band broadens to higher frequency. Since circular dichroism spectra indicate progressive disordering of the chain with increasing salt concentration, we associate the infrared spectral changes with the same phenomenon. Our interpretation of these changes, particularly in the CH₂ bending modes, is that disordering is associated primarily with an increase in the range of accessible C^α–C′ (?O) rotation angles rather than with the random introduction of cis imide bonds in the chain.