Publications by authors named "Brian W Beck"

6 Publications

  • Page 1 of 1

Non-prenylatable, cytosolic Rac1 alters neurite outgrowth while retaining the ability to be activated.

Cell Signal 2015 Mar 2;27(3):630-7. Epub 2014 Dec 2.

Texas Woman's University Department of Biology, Denton, TX 76204-5799, United States. Electronic address:

Rac1 is an important regulator of axon extension, cell migration and actin reorganization. Like all Rho guanine triphosphatases (GTPases), Rac1 is targeted to the membrane by the addition of a geranylgeranyl moiety, an action thought to result in Rac1 guanosine triphosphate (GTP) binding. However, the role that Rac1 localization plays in its activation (GTP loading) and subsequent activation of effectors is not completely clear. To address this, we developed a non-prenylatable emerald green fluorescent protein (EmGFP)-Rac1 fusion protein (EmGFP-Rac1(C189A)) and assessed how expressing this construct affected neurite outgrowth, Rac1 localization and activation in neuroblastoma cells. Expression of EmGFP-Rac1(C189A) increased localization to the cytosol and induced cell clustering while increasing neurite initiation. EmGFP-Rac1(C189A) expression also increased Rac1 activation in the cytosol, compared to cells expressing wild-type Rac1 (EmGFP-Rac1). These results suggest that activation of Rac1 may not require plasma membrane localization, potentially leading to differential activation of cytosolic signaling pathways that alter cell morphology. Understanding the consequences of differential localization and activation of Rho GTPases, including Rac1, could lead to new therapeutic targets for treating neurological disorders.
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http://dx.doi.org/10.1016/j.cellsig.2014.11.033DOI Listing
March 2015

Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins.

PLoS One 2014 15;9(5):e97115. Epub 2014 May 15.

Department of Biology, Texas Woman's University, Denton, Texas, United States of America; Department of Mathematics and Computer Science, Texas Woman's University, Denton, Texas, United States of America; Department of Chemistry and Biochemistry, Texas Woman's University, Denton, Texas, United States of America.

Specific protein interactions are responsible for most biological functions. Distinguishing Functionally Linked Interfaces of Proteins (FLIPs), from Functionally uncorrelated Contacts (FunCs), is therefore important to characterizing these interactions. To achieve this goal, we have created a database of protein structures called FLIPdb, containing proteins belonging to various functional sub-categories. Here, we use geometric features coupled with Kortemme and Baker's computational alanine scanning method to calculate the energetic sensitivity of each amino acid at the interface to substitution, identify hotspots, and identify other factors that may contribute towards an interface being FLIP or FunC. Using Principal Component Analysis and K-means clustering on a training set of 160 interfaces, we could distinguish FLIPs from FunCs with an accuracy of 76%. When these methods were applied to two test sets of 18 and 170 interfaces, we achieved similar accuracies of 78% and 80%. We have identified that FLIP interfaces have a stronger central organizing tendency than FunCs, due, we suggest, to greater specificity. We also observe that certain functional sub-categories, such as enzymes, antibody-heavy-light, antibody-antigen, and enzyme-inhibitors form distinct sub-clusters. The antibody-antigen and enzyme-inhibitors interfaces have patterns of physical characteristics similar to those of FunCs, which is in agreement with the fact that the selection pressures of these interfaces is differently evolutionarily driven. As such, our ECR model also successfully describes the impact of evolution and natural selection on protein-protein interfaces. Finally, we indicate how our ECR method may be of use in reducing the false positive rate of docking calculations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097115PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022497PMC
January 2015

Effects of dimerization of Serratia marcescens endonuclease on water dynamics.

Biopolymers 2007 Feb;85(3):241-52

Department of Chemistry, University of Houston, Houston, TX 77204-5641, USA.

The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.
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http://dx.doi.org/10.1002/bip.20641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583238PMC
February 2007

The N-terminal lobes of both regulatory light chains interact with the tail domain in the 10 S-inhibited conformation of smooth muscle myosin.

J Biol Chem 2006 Dec 29;281(50):38801-11. Epub 2006 Sep 29.

Department of Biochemistry and Molecular Biology, School of Medicine, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA.

In the presence of ATP, unphosphorylated smooth muscle myosin can form a catalytically inactive monomer that sediments at 10 Svedbergs (10 S). The tail of 10 S bends into thirds and interacts with the regulatory domain. ADP-P(i) is "trapped" at the active site, and consequently the ATPase activity is extremely low. We are interested in the structural basis for maintenance of this off state. Our prior photocross-linking work with 10 S showed that tail residues 1554-1583 are proximal to position 108 in the C-terminal lobe of one of the two regulatory light chains ( Olney, J. J., Sellers, J. R., and Cremo, C. R. (1996) J. Biol. Chem. 271, 20375-20384 ). These data suggested that the tail interacts with only one of the two regulatory light chains. Here we present data, using a photocross-linker on position 59 on the N-terminal lobe of the regulatory light chain (RLC), demonstrating that both regulatory light chains of a single molecule can cross-link to the light meromyosin portion of the tail. Mass spectrometric data show four specific cross-linked regions spanning residues 1428-1571 in the light meromyosin portion of the tail, consistent with cross-linking two RLC to one light meromyosin. In addition, we find that position 59 can cross-link internally to residues 42-45 within the same RLC subunit. The internal cross-link only forms in 10 S and not in unphosphorylated heavy meromyosin (lacking the light meromyosin), suggesting a structural rearrangement within the RLC attributed to the interaction of the tail with the head.
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http://dx.doi.org/10.1074/jbc.M606555200DOI Listing
December 2006

Solvent participation in Serratia marcescens endonuclease complexes.

Proteins 2006 Mar;62(4):982-95

Department of Chemistry, University of Houston, Houston, Texas 77204-5641, USA.

The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active and the two subunits of the dimer function independently of each other. Specific interfacial waters may play a role in stability, complex formation, and functionality. We performed molecular dynamics simulations of both a subunit of SMnase and its model built complex with DNA and analyzed the relation of the hydration sites to the catalytic mechanism. It was found that the binding of DNA has little influence on the global hydration properties of the protein, including occupancy and water residence time distributions. DNA and protein recognition in our model mainly involves direct contacts by hydrogen bond and hydrophobic interactions. Water-mediated contacts exist, but are less common. Three interior water clusters were identified for SMnase. One cluster around the active site in the monomer-DNA complex shows relatively strong interactions between hydration sites as well as between the sites and the biomolecules. The simulated cluster properties agreed well with experimental data. The magnesium ion shows ligand exchange. Although Mg2+ keeps six ligands during the entire simulation, upon the binding of DNA, Asn119 loses its coordination with Mg2+, while one nonbridging oxygen of the phosphate of a DNA residue and two oxygen atoms of the side chain of Glu127 become the ligands. Waters in a nearby cluster exchange and participate in the resolvation of groups in the presence of DNA. Water thus not only participates in the cleavage of DNA but also can stabilize the transition state and the leaving groups in our model.
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http://dx.doi.org/10.1002/prot.20694DOI Listing
March 2006

Protein control of electron transfer rates via polarization: molecular dynamics studies of rubredoxin.

Biophys J 2004 Apr;86(4):2030-6

School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.

The protein matrix of an electron transfer protein creates an electrostatic environment for its redox site, which influences its electron transfer properties. Our studies of Fe-S proteins indicate that the protein is highly polarized around the redox site. Here, measures of deviations of the environmental electrostatic potential from a simple linear dielectric polarization response to the magnitude of the charge are proposed. In addition, a decomposition of the potential is proposed here to describe the apparent deviations from linearity, in which it is divided into a "permanent" component that is independent of the redox site charge and a dielectric component that linearly responds or polarizes to the charge. The nonlinearity measures and the decomposition were calculated for Clostridium pasteurianum rubredoxin from molecular dynamics simulations. The potential in rubredoxin is greater than expected from linear response theory, which implies it is a better electron acceptor than a redox site analog in a solvent with a dielectric constant equivalent to that of the protein. In addition, the potential in rubredoxin is described well by a permanent potential plus a linear response component. This permanent potential allows the protein matrix to create a favorable driving force with a low activation barrier for accepting electrons. The results here also suggest that the reduction potential of rubredoxin is determined mainly by the backbone and not the side chains, and that the redox site charge of rubredoxin may help to direct its folding.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304056PMC
http://dx.doi.org/10.1016/S0006-3495(04)74264-2DOI Listing
April 2004