James M. Varnum

Structural modeling in humic acids

Abstract Humic acids are important biological and environmental materials; however, to date there are no significant reports confirming the primary or secondary structure of the building blocks of humic substances. In this work, we report a complementary experimental and computational study that utilizes molecular mechanical applications and spectroscopic tools to evaluate both the primary and secondary structural features of humic acids. The identification of an amide and pronounced CD response suggests a significant secondary structure for humic acids.

The role of metal complexation in the solubility and stability of humic acid

Abstract Humic acid (HA) obtained from a variety of sources displays somewhat varied chemical composition and residual metal content. In spite of extensive purification procedures as much as 0.5% metal (by weight) can remain in the humic acid. In some cases, particularly for Cu 2+ , the metal binding appears site specific, while in others the cupric ion is less strongly bound. Furthermore, the iron content of the samples appears to be dependent on the source and purification procedure. Quantitative removal or exchange of the residual metal is expected to alter the stability and solubility properties of the HA. The treatment of highly purfied HA with Chelex® resin has afforded a material in which the amount of the so-called residual metal has been reduced by 40% or more. This reduction in metal content appears to affect solution aggregation phenomena and consequently the rate of flocculation. Metal removal depends on pre-treatment conditions of the HA sample and is highly pH and temperature dependent. These observations suggest that chemical transformations of HA at high pH and moderate temperature may affect the equilibrium state between the bound metal in HA and the metal-Chelex® complex. The apparently selective removal of metal suggests a specific role of the metal.

Rational design of a peptide analog of the L3T4 CDR3-like region

The CD4 glycoprotein functions in synergy with the T cell receptor complex to generate the signals involved in T cell activation. The exact role CD4 plays in this process is not fully understood. In an attempt to further define the role of CD4 in T helper activation, we developed a structural model of the mouse CD4 (L3T4) based on the X-ray crystal structure of human CD4. From this model a synthetic peptide analog was designed to mimic the surface of the CDR3-like region of L3T4. In general, the inherent flexibility and consequent solution behavior of linear synthetic peptides have limited their application in investigating receptor-ligand interactions. We attempted to overcome these obstacles by limiting the potential peptide conformers using the rigidity of a novel turn motif and a covalent cyclization. The use of small synthetic analogs that mimic the activity of the parent protein allows the dissection of complex proteins into biologically relevant substructures. In this study we have designed an L3T4 CDR3 analog exhibiting highly specific inhibition of L3T4-dependent responses. Since the activity of the peptide maps directly to the T cell, it appears that the analog acts by uncoupling a CD4 association, and suggests a direct involvement of the CDR3-like region in cis-type interaction critical to the transduction of activation signals.