Narinder Singh

Type IV Collagen of the Glomerular Basement Membrane EVIDENCE THAT THE CHAIN SPECIFICITY OF NETWORK ASSEMBLY IS ENCODED BY THE NONCOLLAGENOUS NC1 DOMAINS

The ultrafiltration function of the glomerular basement membrane (GBM) of the kidney is impaired in genetic and acquired diseases that affect type IV collagen. The GBM is composed of five (α1 to α5) of the six chains of type IV collagen, organized into an α1·α2(IV) and an α3·α4·α5(IV) network. In Alport syndrome, mutations in any of the genes encoding the α3(IV), α4(IV), and α5(IV) chains cause the absence of the α3·α4·α5 network, which leads to progressive renal failure. In the present study, the molecular mechanism underlying the network defect was explored by further characterization of the chain organization and elucidation of the discriminatory interactions that govern network assembly. The existence of the two networks was further established by analysis of the hexameric complex of the noncollagenous (NC1) domains, and the α5 chain was shown to be linked to the α3 and α4 chains by interaction through their respective NC1 domains. The potential recognition function of the NC1 domains in network assembly was investigated by comparing the composition of native NC1 hexamers with hexamers that were dissociated and reconstituted in vitro and with hexamers assembled in vitro from purified α1-α5(IV) NC1 monomers. The results showed that NC1 monomers associate to form native-like hexamers characterized by two distinct populations, an α1·α2 and α3·α4·α5 heterohexamer. These findings indicate that the NC1 monomers contain recognition sequences for selection of chains and protomers that are sufficient to encode the assembly of the α1·α2 and α3·α4·α5 networks of GBM. Moreover, hexamer formation from the α3, α4, and α5 NC1 monomers required co-assembly of all three monomers, suggesting that mutations in the NC1 domain in Alport syndrome may disrupt the assembly of the α3·α4·α5 network by interfering with the assembly of the α3·α4·α5 NC1 hexamer.

[9] Calorimetric methods for interpreting protein—Ligand interactions☆

Publisher Summary This chapter discusses the calorimetric methods for interpreting protein-ligand interactions. Calorimetric measurement of protein-ligand binding is considered from two different viewpoints: one is its use in obtaining binding constants, the other is its employment to measure the other thermodynamic parameters of a reaction. Heat uses as a phenomenological signal to indicate the extent to which a ligand-binding site is saturated. Calorimetry merely takes its place among a wide variety of such physically measurable signals whose utility in determining binding constants requires no knowledge of the physical basis of its expression. As such, like other signals (such as difference spectroscopy, fluorescence, H + titration, and elution gel chromatography), its choice of employment in the measurement of K depends on two kinds of factors, intrinsic factors and the specific system. The enthalpy of a given protein-ligand interaction is a function of ligand concentration, pH, and temperature, as well as the presence of other ligands, ionic strength, and other solvent conditions.

A slow obligatory proton release step precedes hydride transfer in the liver glutamate dehydrogenase catalytic mechanism

We have used the stopped-flow indicator dye method to measure proton release and product formation simultaneously in the initial transient-state portion of the glutamate dehydrogenase-catalyzed oxidative deamination of L-glutamate. We observe a measurably slow release of a proton from the enzyme-NADP-L-glutamate complex. This proton release precedes the hydride transfer step, as indicated by the distinct lag in the product formation signal. We show that the proton release step corresponds to an obligatory intermediate in the reaction sequence. We also find that compounds which are competitive inhibitors of L-glutamate are capable of inducing this phenomenon. We prove that this unanticipated prehydride transfer event cannot be due to the release of an alpha-amino group proton from the substrate.

Transduction of enzyme-ligand binding energy into catalytic driving force

We propose a testable general mechanism by which ligand binding energy can be used to drive a catalytic step in an enzyme catalyzed reaction or to do other forms of work involving protein molecules. This energy transduction theory is based on our finding of the widespread occurrence of ligand binding‐induced protein macrostate interconversions each having a large invariant ΔH° accompanied by a small but highly variable ΔG°. This phenomenon, which can be recognized by the large ΔCp°s it generates, can provide the necessary energy input step but is not in itself sufficient to constitute a workable transduction mechanism. A viable mechanism requires the additional presence of an ‘energy transmission step’ which is terminated to trigger the ‘power’ stroke at a precise location on the reaction coordinate, followed by an energetically inexpensive ‘return’ step to restore the machine to its initial conditions. In the model we propose here, these additional steps are provided by the existence of ligand inducible 2‐state transitions in the free enzyme and in each of the enzyme complexes that occur along the reaction coordinate, and by the selective blocking of certain of these interconversions by high energetic barriers. We provide direct experimental evidence supporting the facts that these additional mechanistic components do exist and that the liver glutamate dehydrogenase reaction is indeed driven by just such machinery. We describe some aspects of the chemical nature of these transitions, and evidence for their occurrence in other systems.

The Meaning of Interaction Parameters in Two-State Protein Complexes

The theory of interaction parameters has thus far been based on the free-energy relationships in the formation of ternary complexes formed between a pair of ligands and a protein molecule. The concept has been formulted in terms of a ‘thermodynamic square’ comprised of the free protein, the two binary complexes, and the ternary complex. However, an increasing number of proteins have been found to exist as equilibrium mixtures of two macrostates. The equilibrium constants for such two-state transitions vary quite considerably between the various binary and ternary complexes of a given protein. We show here that the interpretations of interaction parameters in such two-state systems, requiring the use of a ‘thermodynamic cube’, are much more complex than those based on the classic ‘thermodynamic square’ commonly employed. We demonstrate the use of enthalpies of interaction and heat capacities of interaction to analyze the source of observed free enerigies of interaction in such systems. Specifically, we find that measured negative interaction parameters may arise simply from the inability of a system to achieve all of the positive component effects anticipated by the conventional formulation.