Andrew J Rader

Publications (30) View all

• Source

  Available from: Jeffrey D Wolt

  Article: Thermostability in endoglucanases is fold-specific.

  Ragothaman M Yennamalli, Andrew J Rader, Jeffrey D Wolt, Taner Z Sen
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  ABSTRACT: Endoglucanases are usually considered to be synergistically involved in the initial stages of cellulose breakdown-an essential step in the bioprocessing of lignocellulosic plant materials into bioethanol. Despite their economic importance, we currently lack a basic understanding of how some endoglucanases can sustain their ability to function at elevated temperatures required for bioprocessing, while others cannot. In this study, we present a detailed comparative analysis of both thermophilic and mesophilic endoglucanases in order to gain insights into origins of thermostability. We analyzed the sequences and structures for sets of endoglucanase proteins drawn from the Carbohydrate-Active enZymes (CAZy) database. Our results demonstrate that thermophilic endoglucanases and their mesophilic counterparts differ significantly in their amino acid compositions. Strikingly, these compositional differences are specific to protein folds and enzyme families, and lead to differences in intramolecular interactions in a fold-dependent fashion. Here, we provide fold-specific guidelines to control thermostability in endoglucanases that will aid in making production of biofuels from plant biomass more efficient.
  BMC Structural Biology 02/2011; 11:10. · 2.48 Impact Factor
• Article: Correlating allostery with rigidity.

  A J Rader, Stephen M Brown
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  ABSTRACT: Allosteric proteins demonstrate the phenomenon of a ligand binding to a protein at a regulatory or effector site and thereby changing the chemical affinity of the catalytic site. As such, allostery is extremely important biologically as a regulatory mechanism for molecular concentrations in many cellular processes. One particularly interesting feature of allostery is that often the catalytic and effector sites are separated by a large distance. Structural comparisons of allosteric proteins resolved in both inactive and active states indicate that a variety of structural rearrangement and changes in motions may contribute to general allosteric behavior. In general it is expected that the coupling of catalytic and regulatory sites is responsible for allosteric behavior. We utilize a novel examination of allostery using rigidity analysis of the underlying graph of the protein structures. Our results indicate a general global change in rigidity associated with allosteric transitions where the R state is more rigid than the T state. A set of allosteric proteins with heterotropic interactions is used to test the hypothesis that catalytic and effector sites are structurally coupled. Observation of a rigid path connecting the effector and catalytic sites in 68.75% of the structures points to rigidity as a means by which the distal sites communicate with each other and so contribute to allosteric regulation. Thus structural rigidity is shown to be a fundamental underlying property that promotes cooperativity and non-locality seen in allostery.
  Molecular BioSystems 11/2010; 7(2):464-71. · 3.53 Impact Factor
• Article: Thermostability in rubredoxin and its relationship to mechanical rigidity.

  A J Rader
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  ABSTRACT: The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.
  Physical Biology 01/2009; 7:16002. · 2.60 Impact Factor
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  Available from: Andrew J Rader

  Article: Comparisons of protein family dynamics.

  A J Rader, Joshua T Harrell
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  ABSTRACT: Similarities between different protein structures have led to the identification of protein families based upon some measure of structural similarity. Using these similarities one can classify proteins into structural families and higher-order groupings from which inferred function can be transferred. When taken for a large number of proteins, these schemes point to evolutionary relationships between organisms. We propose a novel classification scheme based upon the structurally-inspired dynamics of each protein. This classification scheme has the advantages of being quantitative, automatically assigned, and able to also make distinctions within protein families. Results are presented for five protein families illustrating the correct identification of previously un-classified structures and sources of intrafamily distinctions.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 02/2008;
• Source

  Available from: Andrew J Rader

  Article: Predisposition of the dark state of rhodopsin to functional changes in structure.

  Basak Isin, A J Rader, Harpreet Kaur Dhiman, Judith Klein-Seetharaman, Ivet Bahar
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  ABSTRACT: As the only member of the family of G-protein-coupled receptors for which atomic coordinates are available, rhodopsin is widely studied for insight into the molecular mechanism of G-protein-coupled receptor activation. The currently available structures refer to the inactive, dark state, of rhodopsin, rather than the light-activated metarhodopsin II (Meta II) state. A model for the Meta II state is proposed here by analyzing elastic network normal modes in conjunction with experimental data. Key mechanical features and interactions broken/formed in the proposed model are found to be consistent with the experimental data. The model is further tested by using a set of Meta II fluorescence decay rates measured to empirically characterize the deactivation of rhodopsin mutants. The model is found to correctly predict 93% of the experimentally observed effects in 119 rhodopsin mutants for which the decay rates and misfolding data have been measured, including a systematic analysis of Cys-->Ser replacements reported here. Based on the detailed comparison between model and experiments, a cooperative activation mechanism is deduced that couples retinal isomerization to concerted changes in conformation, facilitated by the intrinsic dynamics of rhodopsin. A global hinge site is identified near the retinal-binding pocket that ensures the efficient propagation of signals from the central transmembrane region to both cytoplasmic and extracellular ends. The predicted activation mechanism opens the transmembrane helices at the critical G-protein binding cytoplasmic domain. This model provides a detailed, mechanistic description of the activation process, extending experimental observations and yielding new insights for further tests.
  Proteins Structure Function and Bioinformatics 12/2006; 65(4):970-83. · 3.39 Impact Factor