The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: how good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknown structure, it would be useful to predict the likely sites of hydrogen bonding of an unknown protein fragment to a known molecule. The positions of maxima and minima in the electrostatic potential at appropriate distances from the van der Waals surface were calculated for various small molecules, nucleic acid bases, peptide units and amino acid side chains containing groups which can form the biologically important N-H...O=C and N-H...N hydrogen bonds. Their ability to predict the positions of H and O/N in hydrogen bonded complexes, as predicted by optimising the electrostatic interactions of pairs of such molecules constrained by the molecular shapes, was assessed. It is shown that extrema in the electrostatic potential around the isolated molecules give worthwhile predictions for the locations of hydrogen binding partners. For molecules bound by a single N-H...O=C hydrogen bond, the electrostatic maximum associated with the H is usually less than 1 A from an acceptor atom, while a C=O electrostatic minimum is generally less than 1.5 A from the hydrogen bond proton. However, a significant number of hydrogen bonds form to the opposite lone pair from the electrostatic minimum, in which case the separation is up to 3.3 A. This reflects the broad electrostatic potential well around a carbonyl oxygen between the lone pair directions. The model predicts when neighbouring atoms drastically change the hydrogen bonding characteristics of an N-H or C=O group. Although the geometries of hydrogen bonded complexes are influenced by the other van der Waals contacts between the molecules, particularly multiple hydrogen bonds, these influences are constant when considering hydrogen bonding to a specific uncharacterised binding site. Hence, the consideration of sterically accessible electrostatic extrema will be useful in the design of new ligands.     

Hysteresis in force probe measurements: a dynamical systems perspective

BACKGROUND: This study was designed to investigate the effects of a modified University of Wisconsin (UW) solution supplemented with one of four buffering agents (histidine, bicine [N,N-bis(2-hydroxyethyl)glycine], tricine [N-tris(hydroxymethyl)methylglycine], and Tris) on liver metabolism during cold ischemic storage. METHODS: Rat livers were flushed and stored for a maximum period of 24 hr at 4 degrees C, and tissue energetics, substrate, and anaerobic end-products were assessed; the group exhibiting the best results during storage was recovered in a 60-min period of warm reperfusion. Relative buffering capacities of the experimental solutions (measured over physiological pH range, in mM H+/L) were: UW, 4.1; histidine+UW, 9.8; Tris+UW, 19.0; bicine+UW, 22.5; tricine+UW, 26.8. RESULTS: In the UW group, ATP levels dropped rapidly over the first 4 hr; 1.0 micromol/g (40% of initial) remained after 4 hr of storage. By 2 hr, ATP levels in bicine- and tricine-treated groups were 0.5 and 1.1 micromol/g greater than in the UW-stored livers and by 10 hr, ATP in bicine-treated livers was twofold that of the control (UW) group. Total adenylate levels also reflected a superior elevation of cellular energetics; even after 24 hr, quantities were 1.4 and 2.0 micromol/g higher than the UW group in bicine- and histidine-supplemented organs. The increase in energetics occurred as a result of increased flux through the major anaerobic energy-producing pathway, glycolysis. The glycolytic rate was significantly greater at storage times > 10 hr with solutions supplemented with bicine, histidine, and tricine. Final values for net lactate accumulation over the entire 24-hr storage period were: UW, 10.1 micromol/g; histidine, 14.3 micromol/g; bicine, 15.2 micromol/g; tricine, 13.8 micromol/g. Activities of glycogen phosphorylase revealed that the activity of this enzyme dropped by 50% within 2 hr of storage in UW. However, histidine and bicine supplementation resulted in a substantial elevation of phosphorylase "a" over 4 hr and 10 hr, respectively. The best buffer of the four examined in this study was bicine; energetics, glycolytic flux, and patterns of adenylate regeneration upon reperfusion were markedly superior to modified UW solution. CONCLUSION: The results of this study suggest that supplementing the "gold standard" UW solution with an additional buffering agent (in order of efficacy: bicine>tricine>histidine) may improve the metabolic status of livers during clinical organ retrieval/storage.     

Designing of peptides with immuno-modulatory properties using protein A as a probe

A series of reports from our laboratory have described the multifarious properties of protein A of Staphylococcus aureus Cowan I, apart from its IgG binding affinity. Original reports regarding its anti-tumor, anti-toxic, anti-carcinogenic and immunomodulatory properties published earlier by the authors have implicated some uniqueness of this bacterial protein. It was conceived that such diversified properties must lie in its specific peptide sequences, rendering it to act and behave as a multipotent "Biological Response Modifier" (BRM). The high resolution X-ray structure of protein A-Fc complex has been delineated earlier, and has been the foundation of many protein engineering studies. This structure along with the amino acid sequence data of its four repetitive domains provided us the basis for designing an octapeptide. This octapeptide was synthesized by solid phase peptide synthesis considering it as the probable site through which PA binds IgG. This octapeptide (NH2-Gln-Asn-Ala-Phe-Tyr-Glu-Ile-Leu-COOH) is present in the first helical segment of B-domain of protein A, and also is a part of domain D, A and C. This octapeptide has been shown to bind IgG by the immunoblotting technique. The binding affinity of the octapeptide appears to be significantly higher than that of intact protein A, as was revealed by calculation of Ka (association constant) and Kd (dissociation constant) values. This octapeptide might serve as a good immunoadsorbant for IgG and/or immune complexes.     

Concepts, properties, and applications of linear systems to describe distribution, identify input, and control endogenous substances and drugs in biological systems

The response at time t (R(t)) of a (causal linear time invariant) system to an input A(t) is represented by: [equation: see text] where K(t) is called the unit impulse response function of the system, and the integration on the right side of the equation (above) is called the convolution (from the latin cum volvere: to interwine) of A(t) and K(t). The system described by this equation is at zero (initial conditions) when t = 0. Although it does not even begin to describe the incredible variety of possible responses of biological systems to inputs, this representation has large applicability in biology. One of the most frequently used applications is known as deconvolution: to deinterwine R(t) given a known K(t) (or A(t)) and observations of R(t), to obtain A(t) (or K(t)). In this paper attention is focused on a greater variety of aspects associated with the use of linear systems to describe biological systems. In particular I define causal linear time-invariant systems and their properties and review the most important classes of methods to solve the deconvolution problem, address. The problem of model selection, the problem of obtaining statistics and in particular confidence bands for the estimated A(t) (and K(t)), and the problem of deconvolution in a population context is also addressed, and so is the application of linear system analysis to determine fraction of input absorbed (bioavailability). A general model to do so in a multiinput-site linear system is presented. Finally the application of linear system analysis to control a biological system, and in particular to target a desired response level, is described, and a general method to do so is presented. Applications to simulated, endocrinology, and pharmacokinetics data are reported.     

Water diffusion in biological porous systems: a NMR approach

The spin-echo nuclear magnetic resonance (NMR) technique together with paramagnetic ion doping are used to study structural parameters of plant samples, such as restricted dimensions, and cell interconnection both through membranes and by cell contact by studying simultaneous restricted diffusion and intercellular water transfer via various pathways. Also, peculiarities of water diffusion on the surface of cell-wall cellulose are studied over a wide range of water content.     

The functional properties of hemoglobin modified with mellitic dianhydride: possible applications as a blood substitute

Human oxyhemoglobin reacts with mellitic dianhydride to produce a modified protein which shows a reduced oxygen affinity over a wide pH range, a reduced but significant cooperativity, a reduced Bohr effect and no response to the allosteric effectors: chloride, clofibric acid or inositol hexaphosphate. The amount of crosslinking in the modified hemoglobin is approximately 22% suggesting promise as a blood substitute. Reaction of deoxyhemoglobin with mellitic dianhydride produces a modified protein with reduced response to clofibric acid and a decrease in oxygen affinity in the presence of inositol hexaphosphate.     

Recent developments in solid-state nuclear magnetic resonance of quadrupolar nuclei and applications to biological systems

Recent advances in nuclear magnetic resonance (NMR) methodology and improvements in high-field NMR instrumentation have generated a new wave of research interests in the application of solid-state NMR to the study of quadrupolar nuclei. These developments now permit increasingly complex biological systems to be probed by quadrupolar NMR. In this review I describe a few recent developments in NMR studies of quadrupolar nuclei and demonstrate the potential of solid-state quadrupolar NMR in the study of biological systems. In particular, I discuss the application of solid-state NMR of (17)O, 67Zn, 59Co, 23Na, and 39K nuclei with a prognosis for future work.     

Effects of hydrogen bonding to a bacteriochlorophyll-bacteriopheophytin dimer in reaction centers from Rhodobacter sphaeroides

The properties of the primary electron donor in reaction centers from Rhodobacter sphaeroides have been investigated in mutants containing a bacteriochlorophyll (BChl)--bacteriopheophytin (BPhe) dimer with and without hydrogen bonds to the conjugated carbonyl groups. The heterodimer mutation His M202 to Leu was combined with each of the following mutations: His L168 to Phe, which should remove an existing hydrogen bond to the BChl molecule; Leu L131 to His, which should add a hydrogen bond to the BChl molecule; and Leu M160 to His and Phe M197 to His, each of which should add a hydrogen bond to the BPhe molecule [Rautter, J., Lendzian, F., Schulz, C., Fetsch, A., Kuhn M., Lin, X., Williams, J. C., Allen J. P., & Lubitz, W. (1995) Biochemistry 34, 8130-8143]. Pigment extractions and Fourier transform Raman spectra confirm that all of the mutants contain a heterodimer. The bands in the resonance Raman spectra arising from the BPhe molecule, which is selectively enhanced, exhibit the shifts expected for the addition of a hydrogen bond to the 9-keto and 2-acetyl carbonyl groups. The oxidation--reduction midpoint potential of the donor is increased by approximately 85 mV by the addition of a hydrogen bond to the BChl molecule but is only increased by approximately 15 mV by the addition of a hydrogen bond to the BPhe molecule. An increase in the rate of charge recombination from the primary quinone is correlated with an increase in the midpoint potential. The yield of electron transfer to the primary quinone is 5-fold reduced for the mutants with a hydrogen bond to the BPhe molecule. Room- and low-temperature optical absorption spectra show small differences from the features that are typical for the heterodimer, except that a large increase in absorption is observed around 860-900 nm for the donor Qy band in the mutant that adds a hydrogen bond to the BChl molecule. The changes in the optical spectra and the yield of electron transfer are consistent with a model in which the addition of a hydrogen bond to the BChl molecule increases the energy of an internal charge transfer state while the addition to the BPhe molecule stabilizes this state. The results show that the properties of the heterodimer are different depending on which side is hydrogen-bonded and suggest that the hydrogen bonds alter the energy of the internal charge transfer state in a well-defined manner.     

Characterization of hydrogen bonding in the complex of adenosine deaminase with a transition state analogue: a Raman spectroscopic study

The Raman spectra of purine ribonucleoside as well as a stable model compound (1-methoxyl-1,6-dihydropurine ribonucleoside), free in solution and bound into its complex with adenosine deaminase (ADA), have been studied by Raman difference spectroscopy. Using purine riboside analogues labeled with 15N1 or 13C6 and the theoretical frequency normal-mode analyses of these molecules using ab initio quantum mechanic methods, we have positively identified many of the Raman bands in the enzyme-bound inhibitor. The spectrum of the enzyme-bound inhibitor is consistent with the enzyme-catalyzed hydration of the purine base to yield 1-hydroxyl-1,6-dihydropurine ribonucleoside, as suggested earlier by X-ray crystallographic studies. In addition, the Raman data and subsequent vibrational analyses show that the binding-induced Raman spectral changes of the inhibitor can be modeled by the formation of a strong hydrogen bond to its N1-H bond. This hydrogen bond, apparently between the N1-H of the inhibitor and the Odelta1 of Glu217 in ADA, causes a substantial N1-H bending frequency increase of about 50-100 cm-1 compared to its solution value, and this results in an estimated enthalpy of the hydrogen bond of 4-10 kcal/mol. The relationship of transition state stabilization in the catalytic strategy of this efficient enzyme to such a bonding pattern is discussed.     

Use of biotinylated-cysteinyl-tRNA as a non-RI probe in protein synthesis

A convenient method for the preparation of biotinylated aminoacyl-tRNA to use in the non-radioisotopic (non-RI) detection of cell-free translation products was developed. After aminoacylation of E. coli tRNA(Cys) with L-cystein, its sulfhydryl group was modified with N-(6-[Biotinamide]hexyl)-3'-(2'-pyridyl dithio) propionamide or 1-Biotin amido-4-(4'-[maleimidomethyl] cyclohexane-carboxamido) butane. These biotin-labelled cysteinyl-tRNA are expected to function as the non-RI probe for protein synthesis equally to or even better than the biotinylated lysyl-tRNA which is now commercially available.     

Mechanism and potential applications of bio-ligninolytic systems in a CELSS

A large amount of inedible plant material, generated as a result of plant growth in a Controlled Ecological Life Support System (CELSS), should be pretreated and converted into forms that can be recycled on earth as well as in space. The main portion of the inedible biomass is lignocellulosic material. Enzymatic hydrolysis of this cellulose would provide sugars for many other uses by recycling carbon, hydrogen, oxygen, and nitrogen through formation of carbon dioxide, heat, and sugars, which are potential foodstuffs. To obtain monosaccharides from cellulose, the protective effect of lignin should be removed. White-rot fungi degrade lignin more extensively and rapidly than other microorganisms. Pleurotus ostreatus degrades lignin effectively, and produces edible and flavorful mushrooms that increase the quality and nutritional value of the diet. This mushroom is also capable of metabolizing hemicellulose, thereby providing a food use of this pentose containing polysaccharide. This study presents the current knowledge of physiology and biochemistry of primary and secondary metabolisms of basidiomycetes, and degradation mechanism of lignin. A better understanding of the ligninolytic activity of white-rot fungi will impact the CELSS Program by providing insights on how edible fungi might be used to recycle the inedible portions of the crops.