Biomedical subjects

L Laaksonen

Publications and source records attributed to L Laaksonen.

7 recordsLinked to original sources

PubMed2001

Molecular mechanism for agonist-promoted alpha(2A)-adrenoceptor activation by norepinephrine and epinephrine.

We present a mechanism for agonist-promoted alpha(2A)-adrenergic receptor (alpha(2A)-AR) activation based on structural, pharmacological, and theoretical evidence of the interactions between phenethylamine ligands and alpha(2A)-AR. In this study, we have: 1) isolated enantiomerically pure phenethylamines that differ both in their chirality about the beta-carbon, and in the presence/absence of one or more hydroxyl groups: the beta-OH and the catecholic meta- and para-OH groups; 2) used [(3)H]UK-14,304 [5-bromo-N-(4,5-dihydro-1H-imidazol-2-yl)-6-quinoxalinamine; agonist] and [(3)H]RX821002 [2-(2-methoxy-1,4-benzodioxan-2-yl)-2-imidazoline; antagonist] competition binding assays to determine binding affinities of these ligands to the high- and low-affinity forms of alpha(2A)-AR; 3) tested the ability of the ligands to promote receptor activation by measuring agonist-induced stimulation of [(35)S]GTPgammaS binding in isolated cell membranes; and 4) used automated docking methods and our alpha(2A)-AR model to predict the binding modes of the ligands inside the alpha(2A)-AR binding site. The ligand molecules are sequentially missing different functional groups, and we have correlated the structural features of the ligands and ligand-receptor interactions with experimental ligand binding and receptor activation data. Based on the analysis, we show that structural rearrangements in transmembrane helix (TM) 5 could take place upon binding and subsequent activation of alpha(2A)-AR by phenethylamine agonists. We suggest that the following residues are important in phenethylamine interactions with alpha(2A)-AR: Asp113 (D(3.32)), Val114 (V(3.33)), and Thr118 (T(3.37)) in TM3; Ser200 (S(5.42)), Cys201 (C(5.43)), and Ser204 (S(5.46)) in TM5; Phe391 (F(6.52)) and Tyr394 (Y(6.55)) in TM6; and Phe411 (F(7.38)) and Phe412 (F(7.39)) in TM7.

Adrenergic Agonists↗

PubMed1997

Visualization of solvation structures in liquid mixtures.

Spatial distribution functions of atomic densities. SDFs, have been proposed as a natural starting point for analysis of local molecular structure in liquids and solutions. The local structure in these systems is often complex and this is reflected in the fact that SDFs can be difficult to visualize. Among the different methods that can be used to visualize SDFs we discuss 3D isodensity surfaces, cross-sections, and 'comic book' animations. We also discuss the possibility of a simultaneous visualization of SDFs and other 3D fields, such as the electron density. These techniques are all intended to emphasize and bring out aspects of SDFs that promote a further understanding of the local molecular structure. OpenGL-based software has been used under X-Windows to implement these techniques, and we argue that high-quality molecular graphics need not be expensive. Data from a molecular dynamics simulation of an equimolar binary mixture of water and acetonitrile have been used to illustrate the discussion.

Computer Graphics↗

PubMed1994

Poliovirus type 3/Saukett: antigenic and structural correlates of sequence variation in the capsid proteins.

The Saukett/USA/50 strain is the type 3 component of the inactivated poliovirus vaccine. The capsid-coding region of genomic RNA of Saukett strains from five different sources was sequenced and the sequence differences were correlated with antigenic differences measurable with poliovirus type 3-specific neutralizing monoclonal antibodies. All strains appeared to have capsid protein genes identical in size to those of the entirely sequenced type 3 poliovirus strains. The nucleotide sequence identity between the strains was 91% on the average and the strains could be divided into three groups. Amino acid differences were seen in 30 positions located throughout the capsid region both within and outside the known antigenic sites. Substitutions at the known antigenic sites explained most of the observed antigenic differences. Use of the atomic coordinates of the crystal structure model of the Sabin 3 virus and prior data based on escape mutants and peptide scanning revealed that most of the exposed substitutions located outside the known antigenic sites are spatially associated with regions found to be antigenic by either or both of these methods.

Antigenic Variation↗

PubMed1993

Cooperative effects in the transport of small molecules through an amorphous polymer matrix.

The transport of small molecules (penetrants) through polymer materials proceeds by a hopping mechanism: A penetrant typically dwells in a cavity of the polymer for a while and then performs a quick jump into an adjacent cavity. In this article we investigate a jump event in detail. Molecular graphics is used to identify if and how the motion of the penetrant is aided by the fluctuations of the polymer matrix. We employ both traditional molecular graphics techniques to show atomic motion and surface rendering methods to display the redistribution of penetrant-accessible volume in the polymer.

Computer Graphics↗

PubMed1992

Investigation of the function of mutated cellulose-binding domains of Trichoderma reesei cellobiohydrolase I.

The function of the cellulose-binding domain (CBD) of the cellobiohydrolase I of Trichoderma reesei was studied by site-directed mutagenesis of two amino acid residues identified by analyzing the 3D structure of this domain. The mutant enzymes were produced in yeast and tested for binding and activity on crystalline cellulose. Mutagenesis of the tyrosine residue (Y492) located at the tip of the wedge-shaped domain to alanine or aspartate reduced the binding and activity on crystalline cellulose to the level of the core protein lacking the CBD. However, there was no effect on the activity toward small oligosaccharide (4-methylumbelliferyl beta-D-lactoside). The mutation tyrosine to histidine (Y492H) lowered but did not destroy the cellulose binding, suggesting that the interaction of the pyranose ring of the substrate with an aromatic side chain is important. However, the catalytic activity of this mutant on crystalline cellulose was identical to the other two mutants. The mutation P477R on the edge of the other face of the domain reduces both binding and activity of CBHI. These results support the hypothesis that both surfaces of the CBD are involved in the interaction of the binding domain with crystalline cellulose.

Adsorption↗

PubMed1992

A graphics program for the analysis and display of molecular dynamics trajectories.

The program SCARECROW has been developed to help the molecular modeler to analyze and display the very big and complex data files produced by molecular dynamics programs. The molecular graphics program SCARECROW is written to support the display, animation, and extensive analysis of molecular dynamics trajectories. Using the macro language it is easy to make scripts for video animation and for the automated display and analysis of time series. Extensive coloring and atom selection commands are included to help the user to focus on relevant regions of the molecule. Time series can be produced and viewed on the screen or transferred to other programs.

Chemical Phenomena↗

PubMed1990

Molecular modelling study of antigen binding to oxazolone-specific antibodies: the Ox1 idiotypic IgG and its mature variant with increased affinity to 2-phenyloxazolone.

Structural models of the variable domains of the murine anti-2-phenyloxazolone IgG (Ox1 idiotype) and its somatic variant, which has higher affinity to the hapten 2-phenyloxazolone, were constructed by computer-aided model building using known structures of highly homologous immunoglobulins as templates. Molecular dynamics simulations were used to dock the hapten between the VL and VH domains. The hapten is predicted to bind to slightly different sites in the two models. Hypotheses concerning the role of a number of preferred mutations in anti-oxazolone variants are presented. These can be tested by mutagenesis and crystallography. In particular, the higher binding affinities of the different antibody variants are shown to correlate with better complementarity of electrostatics. The molecular dynamic simulations also suggest that two mobile tryptophans at the mouth of the pocket may play an important role in the binding of hapten.

Amino Acid Sequence↗