BUSQUEDA CHEMICAL ABSTRACT

ALEJANDRA MARIA ARANGO GALLEGO STIVEN ARREDONDO SOTO CHRISTIAN FELIPE JIMENEZ

UNIVERSIDAD DEL VALLE FACULTAD DE CIENCIAS NATURALES Y EXACTAS DEPARTAMENTO DE QUMICA SANTIAGO DE CALI 2014

CONTENIDO Introduccin..3 Primer Paso......4 Segundo Paso......4 Tercer Paso......4 Cuarto Paso.....5 1. 206147p...5 2. 73950w....6 3. 55355b.....6 Quinto Paso..8 1. 158052y.8 2. 333794d.9

Introduccin Para el mejor entendimiento del Chemical Abstact se buscaron artculos acerca de. El Chemical Abstracts Service, una divisin de la American Chemical Society, una de las mayores bases de datos de sustancias qumicas, referencias, reacciones, proveedores de productos qumicos, resmenes. CAS es la nica organizacin en el mundo, cuyo objetivo es encontrar, recoger y organizar toda la informacin de sustancias qumicas a conocer pblicamente.

PRIMER PASO Se buscaron las palabras relacionadas con el tema asignado en clase (Mecanismos de interaccin Ligando-Protena), luego, dichas palabras se tradujeron a ingls para hacer la respectiva bsqueda en el General Subject. Dichas palabras son: Ligand Binding Sities. Ligand. Recognition Moleular. Ligans Protein Binding.

SEGUNDO PASO En el ndex guide se encontraron las siguientes palabras que indican como buscar el tema en el general subject. LIGANDS: studies of ligands as a class are indexed at this heading (P1138G del index guide) For studies of specific ligands, see those specific heading (P1138G del index guide) PROTEIN SPECIFIC OF CLASS: BINDING: (P1138G)

TERCER PASO Se encontraron en el Chemical Abstract tres temas especficos, los cuales son: 1. Ligand discrimination an inhibition of heme iron autooxidation by myoglobin: site-directed mutagenesis a synthetic gene. 206147p 2. Computer simulations applied to site specific mutagenesis an ligand binding: the use of free energy perturbation methods. 73950w 3. Study of strong to ultratight protein interactions using differential scanning calorimetry. 55355b

CUARTO PASO Segn el nmero de referencia, se encontraron los siguientes resmenes en el chemical abstract. 1. 206147p Globins have evolved under strong selective pressure to overcome the natural tendency of a free heme prosthetic group to bind carbon monoxide (CO) 1000-fold more tightly than atmospheric dioxygen (O$\sb2$). Without protein-directed discrimination between these ligand molecules, the basal production of CO from various catabolic processes would inhibit the reversible transport and storage of oxygen that is necessary for life. Until recently, the exact function of active site residues in globin function has relied on studies of naturally occurring hemoglobin (Hb) mutants and globins from species with divergent active site residues. The desire to probe the role of Mb active site residues in ligand discrimination by manipulation of the protein at the genetic level inspired the total synthesis of a gene for sperm whale myoglobin. Total gene synthesis provided a system which circumvented the sometimes tedious cDNA gene cloning methods and some of the proposed problems associated with the expression of the cDNA clones for human hemoglobin chains and human myoglobin. When inserted into the plasmid pUC19, this construction produces soluble heme containing Mb to $\sim$10% of the total soluble E. coli cell protein. The high-level expression of authentic Mb in E. coli therefore provided the necessary starting point for site-directed mutagenesis efforts designed to probe the role of conserved active site globin residues. Replacement of His64, the distal histidine, with twelve different amino acids by site-directed mutagenesis revealed that virtually every amino acid placed in position 64 of the ligand binding pocket (with the possible exception of Gln) destroyed the ability of Mb to stabilize bound O$\sb2$ since the normal hydrogen bond donor had been removed. Site-directed mutagenesis of Val68 confirmed that this residue is also providing steric constraints on bound CO but not O$\sb2$, clearly indicating the concerted action of two active site residues in protein-ligand recognition. Replacement of Val68 with Phe resulted in an altered ligand pathway as evidenced by decreased O$\sb2$ association and dissociation rates with relatively unchanged CO rates.

Comparison between the His64Gly Mb mutant and the analogous mutations in human Hb $\alpha$ and $\beta$ chains revealed that the Hb $\alpha$ chains are most like Mb, however the distal histidine in $\beta$ chains is essentially unimportant in R state hemoglobin ligand binding. (Abstract shortened with permission of author.) 2. 73950w The protein contribution to the relative binding affinity of the ligands CO and O2 toward myoglobin (Mb) has been simulated using free energy perturbation calculations. The tautomers of the His E7 residue are different for the oxymyoglobin (MbO,) and carboxymyoglobin (MbCO) systems. This was modeled by performing two-step calculations that mutate the ligand and mutate the His E7 tautomers in separate steps. Differences in hydrogen bonding to the O2 and CO ligands were incorporated into the model. The O2 complex was calculated to be 2-3 kcal/mol more stable than the corresponding CO complex when compared to the same difference in an isolated heme control. This value agrees well with the experimental value of 2.0 kcal/mol. In qualitative agreement with experiments, the Fe-C-0 bond is found to be bent (0 = 159.8') with a small tilt (4 = 6.2'). The contributions made by each of the 29 residues - within the 9.0-A radius of the iron atom- to the free energy difference are separated into van der Waals and electrostatic contributions; the latter contributions are dominant. Aside from the proxi- mal histidine and the heme group, the residues having the largest difference in free energy in mutating Mb02 -+ MbCO are His E7, Phe CD1, Phe CD4, Val Ell, and Thr E10. 3. 55355b. Data from differential scanning calorimetry (DSC) may be used to estimate very large binding constants that cannot be conveniently measured by more conventional equilibrium techniques. Thermodynamic models have been formulated to describe interacting systems that involve either one thermal transition (protein-ligand) or two thermal transitions (proteinprotein) and either 1:1 or higher binding stoichiometry. Methods are described for obtaining binding constants and heats of binding by two different methods: calculation or simulation fitting of data. Extensive DSC data on 2'CMP binding to RNase are presented and analyzed by the two methods. It is found that the methods agree when binding sites are
6

completely saturated, but substantial errors arise in the calculation method when site saturation is incomplete and the transition of liganded molecules overlaps that of unliganded molecules. This arises primarily from an inability to determine TM (i.e., the temperature where concentrations of folded and unfolded protein are equal) under weak-binding conditions. Results from simulation show that the binding constants and heats of binding from the DSC method agree quantitatively with corresponding estimates obtained from equilibrium methods when extrapolated to the same temperature. It was also found from the DSC data that the binding constant decreases with increasing concentration of ligand, which might arise from nonideality effects associated with dimerization of 2'CMP. Simulations show that the DSC method is capable of estimating binding constants for ultratight interactions up to perhaps 10(40) M-1 or higher, while most equilibrium methods fail well below 10(10) M-1. DSC data from the literature on a number of interacting systems (trypsin-soybean trypsin inhibitor, trypsin-ovomucoid, trypsin-pancreatic trypsin inhibitor, chymotrypsin-subtilisin inhibitor, subtilisin BPN-subtilisin inhibitor, RNase S protein-RNase S peptide, avidin-biotin, ovotransferrin-Fe3+, superoxide dismutase-Zn2+, alkaline phosphatase-Zn2+, and assembly of regulatory and catalytic subunits of aspartate transcarbamoylase) were analyzed by simulation fitting or by calculation. Apparent single-site binding constants ranged from ca. 10(5) to 10(20) M-1, while the interaction constant for assembly of aspartate transcarbamoylase was estimated as 10(37) in molarity units. For most of these systems, the DSC interaction constants compared favorably with other literature estimates, for some it did not for reasons unknown, while for still others this represented the first estimate. Simulations show that for proteins having two binding sites for the same ligand within a single cooperative unit, ligand rearrangement will occur spontaneously during a DSC scan as the transition temperature of the unliganded protein is approached

QUINTO PASO Se buscaron los resmenes de los artculos de los ltimos aos (1993, 1995) encontrados en el Chemical Abstract relacionados con el tema asignado en clase. Dichos artculos son:

1. -

Numero de resumen: 158052y

Titulo: An approximate but efficient method to calculate free energy trends by computer simulations: Application to dihydrofolate reductase-inhibitor complexes. Nombre de autores: Paul R. Gerber, Alan E. Marx, Wilfred F. van Gunsteren. Institucin y pas : Hoffman-La Roche AG, Basle,Switz. Fecha de publicacin: 1993. Idioma: Ingls. Revista: Pharm. Res. Dev.

2. -

Paginas de inters: 305 - 23

Numero de resumen: 333794d. Titulo: [3H] RS - 45041-190: a selective high-affinity radioligand for I2 imidazoline receptors. Nombre de autores: Alison C. MacKinnon, Wiliam S. Redfern, Chritine M. Brown.
Institucin y pas: Departament of Pharmacolology, SIntex Research Centre, Edinburgh, UK. Fecha de publicacin: 1995. Idioma: Ingls. Revista: Br. J. Pharmacol.

Paginas de inters: 1729 36.

Los resumes encontrados:

158052y Derivatives of free energy differences have been calculated by molecular dynamics techniques. The systems under study were ternary complexes of Trimethoprim (TMP) with dihydrofolate reductases of E. coli and chicken liver, containing the cofactor NADPH. Derivatives are taken with respect to modification of TMP, with emphasis on altering the 3-, 4- and 5-substituents of the phenyl ring. A linear approximation allows the encompassing of a whole set of modifications in a single simulation, as opposed to a full perturbation calculation, which requires a separate simulation for each modification. In the case considered here, the proposed technique requires a factor of 1000 less computing effort than a full free energy perturbation

calculation. For the linear approximation to yield a significant result, one has to find ways of choosing the perturbation evolution, such that the initial trend mirrors the full calculation. The generation of new atoms requires a careful treatment of the singular terms in the non-bonded interaction. The result can be represented by maps of the changed molecule, which indicate whether complex formation is favoured under movement of partial charges and change in atom polarizabilities. Comparison with experimental measurements of inhibition constants reveals fair agreement in the range of values covered. However, detailed comparison fails to show a significant correlation. Possible reasons for the most pronounced deviations are given.

333794d (4-chloro-2-(imidazolin-2-yl)isoindoline) is an I2 imidazoline receptor ligand with the highest affinity and selectivity so far described; [3H]-RS-45041-190 has a tritium atom attached to the 7-position on the isoindoline ring. 2. [3H]RS-45041-190 binding to rat kidney membranes was saturable (Bmax = 223.1 +/- 18.4 fmol mg-1 protein) and of high affinity (Kd = 2.71 +/- 0.59 nM). Kinetic studies revealed that the binding was rapid and reversible, with [3H]-RS-45041-190 interacting with two sites or two affinity states. 3. Competition studies showed that 60-70% of [3H]-RS-45041-190 binding (1 nM) was specifically to imidazoline binding sites of the I2 subtype, characterized by high affinity for idazoxan (pIC50 7.85 +/- 0.03) and cirazoline (pIC50 8.16 +/- 0.05). The remaining 30-40% was displaced specifically by the monoamine oxidase A inhibitors, clorgyline and pargyline. 4. alpha 1- and alpha 2-adrenoceptor, I1 imidazoline, histamine, 5-hydroxytryptamine or dopamine receptor ligands had low affinity suggesting that [3H]-RS-45041-190 did not label receptors of these classes. 5. In autoradiography studies, [3H]-RS-45041-190 labelled discrete regions of rat brain corresponding to the distribution of I2 subtypes, notably the subfornical organ, arcuate nucleus, interpeduncular nucleus, medial habenular nucleus and lateral mammillary nucleus, and additional sites in the locus coeruleus, dorsal raphe and dorsomedial hypothalamic nucleus. 6. [3H]-RS-45041-190 therefore labels I2 receptors with high affinity, and an additional site which has high affinity for some monoamine oxidase inhibitors.