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- Selected Peer-reviewed Publications (8)
- Articles (6)
- Peptide binding (2)
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- Base-amino acid (1)
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- Individual DNA base-amino acid (1)
- Lattice calculation (1)
- Modified hammerhead ribozyme (1)
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- Protein sequence homology (1)
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- RNA bulge entropies (1)
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Articles 1 - 15 of 15
Full-Text Articles in Life Sciences
Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede
Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede
Daryl K. Eggers
The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …
Novel Application Of Query-Based Qualitative Predictors For Characterization Of Solvent Accessible Residues In Conjunction With Protein Sequence Homology. Proceedings Of The 22nd International Workshop On Database And Expert Systems Applications, D Rose, R Nepal, S Gholizadeh, R Mishra, R Lau, Brooke Lustig
Novel Application Of Query-Based Qualitative Predictors For Characterization Of Solvent Accessible Residues In Conjunction With Protein Sequence Homology. Proceedings Of The 22nd International Workshop On Database And Expert Systems Applications, D Rose, R Nepal, S Gholizadeh, R Mishra, R Lau, Brooke Lustig
Brooke S. Lustig
No abstract provided.
A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers
A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers
Daryl K. Eggers
A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …
Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight
Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight
Daryl K. Eggers
This study examines the properties of a 4 × 2 matrix of aqueous cations and anions at concentrations up to 8.0 M. The apparent molar water volume, as calculated by subtracting the mass and volume of the ions from the corresponding solution density, was found to exceed the molar volume of ice in many concentrated electrolyte solutions, underscoring the nonideal behavior of these systems. The solvent properties of water were also analyzed by measuring the solubility of diketopiperazine (DKP) in 2.000 M salt solutions prepared from the same ion combinations. Solution rankings for DKP solubility were found to parallel the …
Favourable Influence Of Hydrophobic Surfaces On Protein Structure In Porous Organically-Modified Silica Glasses, Daryl K. Eggers, B. Menaa, M. Herrero, V. Rives, M. Lavrenko
Favourable Influence Of Hydrophobic Surfaces On Protein Structure In Porous Organically-Modified Silica Glasses, Daryl K. Eggers, B. Menaa, M. Herrero, V. Rives, M. Lavrenko
Daryl K. Eggers
Organically-modified siloxanes were used as host materials to examine the influence of surface chemistry on protein conformation in a crowded environment. The sol–gel materials were prepared from tetramethoxysilane and a series of monosubstituted alkoxysilanes, RSi(OR′)3, featuring alkyl groups of increasing chain length in the R-position. Using circular dichroism spectroscopy in the far-UV region, apomyoglobin was found to transit from an unfolded state to a native-like helical state as the content of the hydrophobic precursor increased from 0 to 15%. At a fixed molar content of 5% RSi(OR′)3, the helical structure of apomyoglobin increased with the chain length of the R-group, …
Protein Adsorption Onto Organically-Modified Silica Glass Leads To A Different Structure Than Sol-Gel Encapsulation, Daryl K. Eggers, B, Menaa, C. Torres, M. Herrero, V. Rives, A. R.W Gilbert
Protein Adsorption Onto Organically-Modified Silica Glass Leads To A Different Structure Than Sol-Gel Encapsulation, Daryl K. Eggers, B, Menaa, C. Torres, M. Herrero, V. Rives, A. R.W Gilbert
Daryl K. Eggers
The secondary structures of two proteins were examined by circular dichroism spectroscopy after adsorption onto a series of organically modified silica glasses. The glasses were prepared by the sol-gel technique and were varied in hydrophobicity by incorporation of 5% methyl, propyl, trifluoropropyl, or n-hexyl silane. Both cytochrome c and apomyoglobin were found to lose secondary structure after adsorption onto the modified glasses. In the case of apomyoglobin, the α-helical content of the adsorbed protein ranged from 21% to 28%, well below the 62% helix found in solution. In contrast, these same glasses led to a striking increase in apomyoglobin structure …
Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha
Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha
Daryl K. Eggers
Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique
Protein Sequence Entropy Is Closely Related To Packing Density And Hydrophobicity, H Liao, W Yeh, D Chiang, R L. Jernigan, Brooke Lustig
Protein Sequence Entropy Is Closely Related To Packing Density And Hydrophobicity, H Liao, W Yeh, D Chiang, R L. Jernigan, Brooke Lustig
Brooke S. Lustig
We investigated the correlation between the Shannon information entropy, ‘sequence entropy’, with respect to the local flexibility of native globular proteins as described by inverse packing density. These are determined at each residue position for a total set of 130 query proteins, where sequence entropies are calculated from each set of aligned residues. For the accompanying aggregate set of 130 alignments, a strong linear correlation is observed between the calculated sequence entropy and the corresponding inverse packing density determined at an associated residue position. This region of linearity spans the range of Cα packing densities from 12 to 25 amino …
Flexibility Of Biv Tar-Tat: Models Of Peptide Binding, M Hsieh, E D. Collins, T Blomquist, Brooke Lustig
Flexibility Of Biv Tar-Tat: Models Of Peptide Binding, M Hsieh, E D. Collins, T Blomquist, Brooke Lustig
Brooke S. Lustig
No abstract provided.
Familial Als-Associated Mutations Decrease The Thermal Stability Of Distinctly Metallated Species Of Human Copper/Zinc Superoxide Dismutase, Daryl K. Eggers, J. A. Rodriguez, J. S. Valentine, J. A. Roe, A. Tiwari, R. H. Brown, L. J. Hayward
Familial Als-Associated Mutations Decrease The Thermal Stability Of Distinctly Metallated Species Of Human Copper/Zinc Superoxide Dismutase, Daryl K. Eggers, J. A. Rodriguez, J. S. Valentine, J. A. Roe, A. Tiwari, R. H. Brown, L. J. Hayward
Daryl K. Eggers
We report the thermal stability of wild type (WT) and 14 different variants of human copper/zinc superoxide dismutase (SOD1) associated with familial amyotrophic lateral sclerosis (FALS). Multiple endothermic unfolding transitions were observed by differential scanning calorimetry for partially metallated SOD1 enzymes isolated from a baculovirus system. We correlated the metal ion contents of SOD1 variants with the occurrence of distinct melting transitions. Altered thermal stability upon reduction of copper with dithionite identified transitions resulting from the unfolding of copper-containing SOD1 species. We demonstrated that copper or zinc binding to a subset of “WT-like” FALS mutants (A4V, L38V, G41S, G72S, D76Y, …
Rna Bulge Entropies Correlate With Peptide Binding Strengths For Hiv-1 And Biv Tar Rna Because Of Improved Conformational Access, Brooke Lustig, I Baharand, R L. Jernigan
Rna Bulge Entropies Correlate With Peptide Binding Strengths For Hiv-1 And Biv Tar Rna Because Of Improved Conformational Access, Brooke Lustig, I Baharand, R L. Jernigan
Brooke S. Lustig
For the binding of peptides to wild-type HIV-1 and BIV TAR RNA and to mutants with bulges of various sizes, changes in the ΔΔG values of binding were determined from experimental Kd values. The corresponding entropies of these bulges are estimated by enumerating all possible RNA bulge conformations on a lattice and then applying the Boltzmann relationship. Independent calculations of entropies from fluctuations are also carried out using the Gaussian network model (GNM) recently introduced for analyzing folded structures. Strong correlations are seen between the changes in free energy determined for binding and the two different unbound entropy calculations. The …
Rna Base-Amino Acid Interaction Strengths Derived From Structures And Sequences, Brooke Lustig, S Arora, R L. Jernigan
Rna Base-Amino Acid Interaction Strengths Derived From Structures And Sequences, Brooke Lustig, S Arora, R L. Jernigan
Brooke S. Lustig
We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TARTat complex. We use binding data for the base frequencies for the seryl, aspartyl …
Complexes Between Nascent Polypeptides And Their Molecular Chaperones In The Cytosol Of Mammalian Cells, Daryl K. Eggers, W. J. Welch, W. J. Hansen
Complexes Between Nascent Polypeptides And Their Molecular Chaperones In The Cytosol Of Mammalian Cells, Daryl K. Eggers, W. J. Welch, W. J. Hansen
Daryl K. Eggers
Folding of newly synthesized proteins in vivo is believed to be facilitated by the cooperative interaction of a defined group of proteins known as molecular chaperones. We investigated the direct interaction of chaperones with nascent polypeptides in the cytosol of mammalian cells by multiple methods. A new approach using a polyclonal antibody to puromycin allowed us to tag and capture a population of truncated nascent polypeptides with no bias as to the identity of the bound chaperones. In addition, antibodies that recognize the cytosolic chaperones hsp70, CCT (TRiC), hsp40, p48 (Hip), and hsp90 were compared on the basis of their …
Consistencies Of Individual Dna Base-Amino Acid Interactions In Structures And Sequences, Brooke Lustig, R L. Jernigan
Consistencies Of Individual Dna Base-Amino Acid Interactions In Structures And Sequences, Brooke Lustig, R L. Jernigan
Brooke S. Lustig
Amino acid-amino acid interaction energies have been derived from crystal structure data for a number of years. Here is reported the first derivation of normalized relative interaction from binding data for each of the four bases interacting with a specific amino acid, utilizing data from combinatorial multiplex ONA binding of zinc finger domains [Desjarlais, J. R. and Berg, J. M. (1994) Proc. Natl. Acad. Sci. USA, 91, 11099–11103]. The five strongest Interactions are observed for lysine-guanine, lysine-thymine, arginine- guanine, aspartic acid-cytosine and asparagineadenine. These rankings for interactions with the four bases appear to be related to base-amino acid partial charges. …
A Small Modified Hammerhead Ribozyme And Its Conformational Characteristics Determined By Mutagenesis And Lattice Calculation, Brooke Lustig, N H. Lin, S M. Smith, R L. Jernigan, K.-T Jeang
A Small Modified Hammerhead Ribozyme And Its Conformational Characteristics Determined By Mutagenesis And Lattice Calculation, Brooke Lustig, N H. Lin, S M. Smith, R L. Jernigan, K.-T Jeang
Brooke S. Lustig
A prototypic hammerhead ribozyme has three helices that surround an asymmetrical central core loop. We have mutagenized a hammerhead type ribozyme. In agreement with previous studies, progressive removal of stem-loop II from a three stemmed ribozyme showed that this region is not absolutely critical for catalysis. However, complete elimination of stem II and its loop did reduce, but did not eliminate, function. In a stem-loop II-deleted ribozyme, activity was best preserved when a purine, preferably a G, was present at position 10.1. This G contributed to catalysis irregardless of its role as either one part of a canonical pair with …