Upregulation of alpha(8)beta(1)-integrin in cardiac fibroblast by angiotensin II and transforming growth factor-beta1.

Using a novel pharmacological tool with (125)I-echistatin to detect integrins on the cell, we have observed that cardiac fibroblasts harbor five different RGD-binding integrins: alpha(8)beta(1), alpha(3)beta(1), alpha(5)beta(1), alpha(v)beta(1), and alpha(v)beta(3). Stimulation of cardiac fibroblasts by angiotensin II (ANG II) or transforming growth factor-beta1 (TGF-beta1) resulted in an increase of protein and heightening by 50% of the receptor density of alpha(8)beta(1)-integrin. The effect of ANG II was blocked by an AT(1), but not an AT(2), receptor antagonist, or by an anti-TGF-beta1 antibody. ANG II and TGF-beta1 increased fibronectin secretion, smooth muscle alpha-actin synthesis, and formation of actin stress fibers and enhanced attachment of fibroblasts to a fibronectin matrix. The alpha(8)- and beta(1)-subunits were colocalized by immunocytochemistry with vinculin or beta(3)-integrin at focal adhesion sites. These results indicate that alpha(8)beta(1)-integrin is an abundant integrin on rat cardiac fibroblasts. Its positive modulation by ANG II and TGF-beta1 in a myofibroblast-like phenotype suggests the involvement of alpha(8)beta(1)-integrin in extracellular matrix protein deposition and cardiac fibroblast adhesion.

Comparative specificity of platelet alpha(IIb)beta(3) integrin antagonists.

Several platelet alpha(IIb)beta(3) integrin antagonists have been designed as preventive agents against the formation of arterial thrombi. Although the potency of these compounds in inhibiting platelet aggregation is in the nanomolar range, their specificity on other integrins that can bind ligands through an arginine-glycine-aspartic acid (RGD) motif is far from being well established. For instance, some cyclic RGD peptides can also interact with alpha(v)beta(3) integrin. We used a novel pharmacological assay, based on SDS-stable interaction between (125)I-echistatin and RGD-dependent integrins, to evaluate the specificity of several RGD compounds on integrins present on rat cardiac fibroblasts and human skin fibroblasts. None of the RGD peptidomimetics tested (L-734,217, lamifiban, Ro 44-3888, SR 121566A, BIBU-52, XV459) could interact with either alpha(v)beta(3) and alpha(8)beta(1) on rat fibroblasts or with alpha(v)beta(3) and alpha(v)beta(1) on human fibroblasts. Cyclic RGD peptides showed some potency (3-80 microM) on rat and human integrins with an alpha(v) subunit. We also compared the potency of these compounds on platelets. All RGD compounds demonstrated IC(50) between 0.6 and 530 nM on basal human platelets. Activation of the receptor with thrombin resulted in a 2- to 60-fold increase in potency, with L-734,217 and BIBU-52 showing the largest difference. On basal and thrombin-activated rat platelets, only eptifibatide, DMP728, and XJ735 could displace (125)I-echistatin (IC(50) approximately 0.1-1.5 microM). These results indicate that RGD peptidomimetics have a specificity limited to alpha(IIb)beta(3) integrin, whereas cyclic RGD peptides can also interact with other RGD-dependent integrins, particularly those of the alpha(v) subunit family.

The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

Three-dimensional (3-D) structural models of RNA are essential for understanding of the cellular roles played by RNA. Such models have been obtained by a technique based on a constraint satisfaction algorithm that allows for the facile incorporation of secondary and other structural information. The program generates 3-D structures of RNA with atomic-level resolution that can be refined by numerical techniques such as energy minimization. The precision of this technique was evaluated by comparing predicted transfer RNA loop and RNA pseudoknot structures with known or consensus structures. The root-mean-square deviation (2.0 to 3.0 angstroms before minimization) between predicted and control structures reveal this system to be an effective method in modeling RNA.

FUS: a system to simulate conformational changes in biological macromolecules.

In order to study the dynamics of protein and nucleic acid conformations, a molecular folding-unfolding system (FUS written in Lisp) has been developed. Secondary structure features of protein and nucleic acids are graphically represented by cubes in a modified 'Blocks World' paradigm. Modeling of protein and nucleic acid unfolding (denaturation) and folding of their three-dimensional structure is possible by the use of high level 'block' operators which allow displacement of these structural features in space. Due to the flexible nature of this program, FUS is a useful tool for the rapid evaluation of user-defined rules governing conformational changes. The use of FUS to unfold three common proteins (prealbumin, flavodoxin and triose phosphate isomerase) and a tRNA is presented.

A secondary and tertiary structure editor for nucleic acids.

A major difficulty in the evaluation of secondary and tertiary structures of nucleic acids is the lack of convenient methods for their construction and representation. As a first step in a study of the symbolic representation of biopolymers, we report the development of a structure editor written in Pascal, permitting model construction on the screen of a personal computer. The program calculates energies for helical regions, allows user-defined helices and displays the secondary structure of a nucleic acid based on a user-selected set of helices. Screen and printer outputs can be in the form of a backbone or the letters of the primary sequence. The molecule can then be displayed in a format which simulates its three-dimensional structure. Using appropriate glasses, the molecule can be viewed on the screen in three dimensions. Other options include the manipulation of helices and single-stranded regions which results in changes in the spatial relationship between different regions of the molecule. The editor requires an IBM or compatible PC, 640 kbyte memory and a medium or high resolution graphics card.

An algorithm for the display of nucleic acid secondary structure.

A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples of secondary structure displays are given for tRNA, 5S RNA and part of the 16S RNA. Due to its speed, this algorithm could easily be used in conjunction with secondary structure programs which calculate various alternate structures.

Convergence and minimal mutation criteria for evaluating early events in tRNA evolution.

The convergence of ancestral sequences independently constructed from different branches of a phylogenetic tree can be used as a test of homology of data sequences. This criterion has shown that all phenylalanine tRNAs are related to a common ancestor, whereas eukaryotic and prokaryotic tyrosine tRNAs may have independent origins. All glycine tRNAs share a common ancestor. The glycine tRNA family splits according to the purine or pyrimidine nature of the first anticodon base prior to the divergence of eukaryotes and prokaryotes. The structural similarity between some prokaryotic glycine and and valine tRNAs is the result of their derivation from a common ancestor that existed previous to the divergence of the different glycine tRNAs. These results support models of genetic code evolution involving the incremental elaboration of earlier, simpler codes.

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA.

The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.