temporary banners

 



 

Journal Issue - Volume 7 Issue 8 (August 1998)

Abstract The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modem family of proteins represented by these structures arose...

Abstract Activated Factor X releases F1.2, a 271‐amino acid peptide, from the amino terminus of prothrombin during blood coagulation. A nine‐amino acid peptide, C9 (DSDRAIEGR), corresponding to the carboxyl terminus of F1.2 was synthesized and used to produce a monoclonal antibody, TA1 (KD 1.22 × 10−6 M). To model the TA1 antibody, we entered the sequence information of the cloned TA1 Fv into the antibody modeling program, ABM, which combines...

Abstract A comprehensive deletion, mutational, and structural analysis of the native recombinant keratinocyte growth factor (KGF) polypeptide has resulted in the identification of the amino acids responsible for its biological activity. One of these KGF mutants (A23KGF‐Rl44Q) has biological activity comparable to the native protein, and its crystal structure was determined by the multiple isomorphous replacement plus anomalous...

Abstract Bovine seminal ribonuclease (BS‐RNase) is a unique member of the pancreatic‐like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N‐terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2′,5′)adenosine is reported at 2.06 Å resolution. The...

Abstract The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc...

Abstract Two peptide fragments from tuna cytochrome c (cyt c), N‐fragment (residues 1‐44 containing the heme) and C‐fragment (residues 45‐103), combine to form a 1:1 fragment complex. This was clearly proved by ion‐spray mass spectrometry. It was found from CD and NMR spectra that the structure of the fragment complex formed is similar to that of an intact cyt c, although each isolated fragment itself is unstructured. Binding constants ...

Abstract The protease domain of tissue plasminogen activator (tPA), a key fibrinolytic enzyme, was expressed in Escherichia coli with a yield of 1 mg per liter of media. The recombinant protein was titrated with the Erythrina caraffa trypsin inhibitor (ETI) and characterized in its interaction with plasminogen and the natural inhibitor plasminogen activator inhibitor‐1 (PAI‐1). Analysis of the catalytic properties of tPA using a library of chromogenic...

Abstract Two synthetic analogues of murine epidermal growth factor, [Abu6, 20 mEGF4‐48 (where Abu denotes amino‐butyric acid) and [Gl, M3, K21, H40] mEGF1‐48, have been investigated by NMR spectroscopy. [Abu6, 20] mEGF4‐48 was designed to determine the contribution of the 6‐20 disulfide bridge to the structure and function of mEGF. The overall structure of this analogue was similar to that of native mEGF, indicating that the loss of...

Abstract The changes in the inhibitor binding constants due to the mutation of isoleucine to valine at position 84 of HIV‐1 protease are calculated using molecular dynamics simulations. The calculations are done for three potent inhibitors‐KNI‐272, L‐735,524 (indinavir or MK‐639), and Ro 31‐8959 (saquinavir). The calculations agree with the experimental data both in terms of an overall trend and in the magnitude of the resulting...

Abstract Genetic selection provides an effective way to obtain active catalysts from a diverse population of protein variants. We have used this tool to investigate the role of loop sequences in determining the quaternary structure of a domain‐swapped enzyme. By inserting random loops of four to seven residues into a dimeric chorismate mutase and selecting for functional variants by genetic complementation, we have obtained and...

Abstract Three ATP‐dependent enzymes with different folds, cAMP‐dependent protein kinase, D‐Ala:D‐Ala ligase and the α‐subunit of the α2β2 ribonucleotide reductase, have a similar organization of their ATP‐binding sites. The most meaningful similarity was found over 23 structurally equivalent residues in each protein and includes three strands each from their β‐sheets, in addition to a connecting loop. The equivalent secondary...

Abstract A free energy function, combining molecular mechanics energy with empirical solvation and entropic terms, is used for ranking near‐native conformations that occur in the conformational search steps of homology modeling, i.e., side‐chain search and loop closure calculations. Correlations between the free energy and RMS deviation from the X‐ray structure are established. It is shown that generally both molecular mechanics and...

Abstract Differential chemical modification of the lysines and amino‐terminus of Escherichia coli single‐strand binding (SSB) protein was used to determine their roles in the binding of SSB to single‐stranded DNA (ssDNA). A combination of isotope labeling and mass spectrometry was used to determine the rates at which SSB was acetylated by acetic anhydride. First, SSB was labeled by deuterated acetic anhydride for given lengths of time in the...

Abstract Hydrophilic to hydrophobic mutations have been made at 11 solvent exposed sites on the surface of iso‐1‐cytochrome c. Most of these mutations involve the replacement of lysine with methionine, which is nearly isosteric with lysine. Minimal perturbation to the native structure is expected, and this expectation is confirmed by infrared amide I spectroscopy. Guanidine hydrochloride denaturation studies demonstrate that these variants...

Abstract The 105resolving power and MS/MS capabilities of Fourier‐transform mass spectrometry provide electrospray ionization mass spectra containing > 100 molecular and fragment ion mass values of high accuracy. Applying these spectra to the detection and localization of errors and modifications in the DNA‐derived sequences of proteins is illustrated with the thiCEFSGH thiamin biosynthesis operon from Escherichia coli. Direct fragmentation...

Page:   1 2 Next