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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

The Energy Profiles Of Atomic Conformational Transition Intermediates Of Adenylate Kinase, Yaping Feng, Lei Yang, Andrzej Kloczkowski, Robert L. Jernigan Nov 2009

The Energy Profiles Of Atomic Conformational Transition Intermediates Of Adenylate Kinase, Yaping Feng, Lei Yang, Andrzej Kloczkowski, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

The elastic network interpolation (ENI)1 is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this study, we use ENI to generate conformational transition intermediates between the open form and the closed forms of adenylate kinase (AK). Based on Cα-only intermediates, we construct atomic intermediates by grafting all the atoms of known AK structures onto the Cα atoms and then perform CHARMM energy minimization to remove steric conflicts and optimize ...


Protein Flexibility: Coordinate Uncertainties And Interpretation Of Structural Differences, Alexander A. Rashin, Abraham H. L. Rashin, Robert L. Jernigan Nov 2009

Protein Flexibility: Coordinate Uncertainties And Interpretation Of Structural Differences, Alexander A. Rashin, Abraham H. L. Rashin, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent `noise', showing that some previous interpretations of protein coordinate changes attributed to external ...


Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti Aug 2009

Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti

Biochemistry, Biophysics and Molecular Biology Publications

The Tec family kinase, Itk (interleukin-2 tyrosine kinase), undergoes an in cis autophosphorylation on Y180 within its Src homology 3 (SH3) domain. Autophosphorylation of the Itk SH3 domain by the Itk kinase domain is strictly dependent on the presence of the intervening Src homology 2 (SH2) domain. A direct docking interaction between the Itk kinase and SH2 domains brings the Itk SH3 domain into the active site where Y180 is then phosphorylated. We now identify the residues on the surface of the Itk SH2 domain responsible for substrate docking and show that this SH2 surface mediates autophosphorylation in the full-length ...


Polytene Chromosome Squash Methods For Studying Transcription And Epigenetic Chromatin Modification In Drosophila Using Antibodies, Kristen M. Johansen, Weili Cai, Huai Deng, Xiaomin Bao, Weiguo Zhang, Jack Girton, Jorgen Johansen Aug 2009

Polytene Chromosome Squash Methods For Studying Transcription And Epigenetic Chromatin Modification In Drosophila Using Antibodies, Kristen M. Johansen, Weili Cai, Huai Deng, Xiaomin Bao, Weiguo Zhang, Jack Girton, Jorgen Johansen

Biochemistry, Biophysics and Molecular Biology Publications

The giant polytene chromosomes from Drosophila third instar larval salivary glands provide an important model system for studying the architectural changes in chromatin morphology associated with the process of transcription initiation and elongation. Especially, analysis of the heat shock response has proved useful in correlating chromatin structure remodeling with transcriptional activity. An important tool for such studies is the labeling of polytene chromosome squash preparations with antibodies to the enzymes, transcription factors, or histone modifications of interest. However, in any immunohistochemical experiment there will be advantages and disadvantages to different methods of fixation and sample preparation, the relative merits of ...


Identification Of Light-Independent Inhibition Of Human Immunodeficiency Virus-1 Infection Through Bioguided Fractionation Of Hypericum Perforatum, Wendy Maury, Jason P. Price, Melinda A. Brindley, Choonseok Oh, Jeffrey D. Neighbors, David F. Wiemer, Nickolas Wills, Susan L. Carpenter, Catherine C. Hauck, Patricia A. Murphy, Mark P. Widrlechner, Kathleen Delate, Ganesh Kumar, George A. Kraus, Ludmila Rizshsky, Basil J. Nikolau Jul 2009

Identification Of Light-Independent Inhibition Of Human Immunodeficiency Virus-1 Infection Through Bioguided Fractionation Of Hypericum Perforatum, Wendy Maury, Jason P. Price, Melinda A. Brindley, Choonseok Oh, Jeffrey D. Neighbors, David F. Wiemer, Nickolas Wills, Susan L. Carpenter, Catherine C. Hauck, Patricia A. Murphy, Mark P. Widrlechner, Kathleen Delate, Ganesh Kumar, George A. Kraus, Ludmila Rizshsky, Basil J. Nikolau

NCRPIS Publications and Papers

Background
Light-dependent activities against enveloped viruses in St. John's Wort (Hypericum perforatum) extracts have been extensively studied. In contrast, light-independent antiviral activity from this species has not been investigated.

Results
Here, we identify the light-independent inhibition of human immunodeficiency virus-1 (HIV-1) by highly purified fractions of chloroform extracts of H. perforatum. Both cytotoxicity and antiviral activity were evident in initial chloroform extracts, but bioassay-guided fractionation produced fractions that inhibited HIV-1 with little to no cytotoxicity. Separation of these two biological activities has not been reported for constituents responsible for the light-dependent antiviral activities. Antiviral activity was associated with more ...


Comparisons Of Experimental And Computed Protein Anisotropic Temperature Factors, Lei Yang, Guang Song, Robert L. Jernigan Jul 2009

Comparisons Of Experimental And Computed Protein Anisotropic Temperature Factors, Lei Yang, Guang Song, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as ribosome motions, the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, motor-protein motions, and conformational changes in general. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins obtained from X-ray and NMR data. The rich, directional anisotropic temperature factor data available for hundreds of proteins in the Protein Data Bank (PDB) are used as validation data to closely test ...


Collective Dynamics Of The Ribosomal Tunnel Revealed By Elastic Network Modeling, Ozge Kurkcuoglu, Zeynep Kurkcuoglu, Pemra Doruker, Robert L. Jernigan Jun 2009

Collective Dynamics Of The Ribosomal Tunnel Revealed By Elastic Network Modeling, Ozge Kurkcuoglu, Zeynep Kurkcuoglu, Pemra Doruker, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The low frequency fluctuations indicate three distinct regions along the tunnel - the entrance, the neck and the exit – each having distinctly different domain motions. Generally the lining of the entrance region moves in the exit direction, with the exit region having significantly larger motions, but in a ...


Materials And Methods For The Alteration Of Enzyme And Acetyl Coa Levels In Plants, Basil J. Nikolau, Eve S. Wurtele, David J. Oliver, Patrick S. Schnable, Tsui-Jung Wen Apr 2009

Materials And Methods For The Alteration Of Enzyme And Acetyl Coa Levels In Plants, Basil J. Nikolau, Eve S. Wurtele, David J. Oliver, Patrick S. Schnable, Tsui-Jung Wen

Iowa State University Patents

The present invention provides nucleic acid and amino acid sequences of acetyl CoA synthetase (ACS), plastidic pyruvate dehydrogenase (pPDH), ATP citrate lyase (ACL),Arabidopsis pyruvate decarboxylase (PDC), and Arabidopsis aldehyde dehydrogenase (ALDH), specifically ALDH-2 and ALDH-4. The present invention also provides a recombinant vector comprising a nucleic acid sequence encoding one of the aforementioned enzymes, an antisense sequence thereto or a ribozyme therefor, a cell transformed with such a vector, antibodies to the enzymes, a plant cell, a plant tissue, a plant organ or a plant in which the level of an enzyme has been altered, and a method of ...


Proline Isomerization Preorganizes The Itk Sh2 Domain For Binding The Itk Sh3 Domain, Andrew J. Severin, Raji E. Joseph, Scott E. Boyken, D. Bruce Fulton, Amy H. Andreotti Apr 2009

Proline Isomerization Preorganizes The Itk Sh2 Domain For Binding The Itk Sh3 Domain, Andrew J. Severin, Raji E. Joseph, Scott E. Boyken, D. Bruce Fulton, Amy H. Andreotti

Biochemistry, Biophysics and Molecular Biology Publications

We report here the NMR-derived structure of the binary complex formed by the interleukin-2 tyrosine kinase (Itk) Src homology 3 (SH3) and Src homology 2 (SH2) domains. The interaction is independent of both a phosphotyrosine motif and a proline-rich sequence, the classical targets of the SH2 and SH3 domains, respectively. The Itk SH3/SH2 structure reveals the molecular details of this nonclassical interaction and provides a clear picture for how the previously described prolyl cis/trans isomerization present in the Itk SH2 domain mediates SH3 binding. The higher-affinity cis SH2 conformer is preorganized to form a hydrophobic interface with the ...


Molecular Diagnostic For Boll Weevil (Coleoptera: Curculionidae) Based On Amplification Of Three Species-Specific Microsatellites, Kyung Seok Kim, Zsofia Szendrei, Cesar Rodriguez-Saona, Phillip G. Mulder Jr., Thomas W. Sappington Apr 2009

Molecular Diagnostic For Boll Weevil (Coleoptera: Curculionidae) Based On Amplification Of Three Species-Specific Microsatellites, Kyung Seok Kim, Zsofia Szendrei, Cesar Rodriguez-Saona, Phillip G. Mulder Jr., Thomas W. Sappington

Entomology Publications

The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by scouts. For example, the congeneric pepper weevil,Anthonomus eugenii Cano, and other superficially similar weevils are attracted to components of the boll weevil lure or trap color. Although morphologically distinguishable by trained personnel, the potential for misidentification is compounded when captured weevils are dismembered ...


Spatiotemporal Control Of Mitosis By The Conserved Spindle Matrix Protein Megator, Mariana Lince-Faria, Stefano Maffi, Bernard Orr, Yun Ding, Claudia Florindo, Claudio E. Sunkel, Alvaro Tavares, Jorgen Johansen, Kristen M. Johansen, Helder Maiato Mar 2009

Spatiotemporal Control Of Mitosis By The Conserved Spindle Matrix Protein Megator, Mariana Lince-Faria, Stefano Maffi, Bernard Orr, Yun Ding, Claudia Florindo, Claudio E. Sunkel, Alvaro Tavares, Jorgen Johansen, Kristen M. Johansen, Helder Maiato

Biochemistry, Biophysics and Molecular Biology Publications

A putative spindle matrix has been hypothesized to mediate chromosome motion, but its existence and functionality remain controversial. In this report, we show that Megator (Mtor), the Drosophilamelanogaster counterpart of the human nuclear pore complex protein translocated promoter region (Tpr), and the spindle assembly checkpoint (SAC) protein Mad2 form a conserved complex that localizes to a nuclear derived spindle matrix in living cells. Fluorescence recovery after photobleaching experiments supports that Mtor is retained around spindle microtubules, where it shows distinct dynamic properties. Mtor/Tpr promotes the recruitment of Mad2 and Mps1 but not Mad1 to unattached kinetochores (KTs), mediating ...


Conformational Snapshots Of Tec Kinases During Signaling, Raji E. Joseph, Amy H. Andreotti Mar 2009

Conformational Snapshots Of Tec Kinases During Signaling, Raji E. Joseph, Amy H. Andreotti

Biochemistry, Biophysics and Molecular Biology Publications

The control of cellular signaling cascades is of utmost importance in regulating the immune response. Exquisitely precise protein-protein interactions and chemical modification of substrates by enzymatic catalysis are the fundamental components of the signals that alert immune cells to the presence of a foreign antigen. In particular, the phosphorylation events induced by protein kinase activity must be spatially and temporally regulated by specific interactions to maintain a normal and effective immune response. High resolution structures of many protein kinases along with supporting biochemical data are providing significant insight into the intricate regulatory mechanisms responsible for controlling cellular signaling. The Tec ...


Iterative Cluster-Nma (Icnma): A Tool For Generating Conformational Transitions In Proteins, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, Gregory S. Chirikjian Feb 2009

Iterative Cluster-Nma (Icnma): A Tool For Generating Conformational Transitions In Proteins, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, Gregory S. Chirikjian

Biochemistry, Biophysics and Molecular Biology Publications

Computational models provide insight into the structure-function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this paper, the icNMA method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate ...


Inhibition Of Lentivirus Replication By Aqueous Extracts Of Prunella Vulgaris, Melinda A. Brindley, Mark P. Widrlechner, Joe-Ann Mccoy, Patricia A. Murphy, Catherine C. Hauck, Ludmila Rizshsky, Basil J. Nikolau, Wendy Maury Jan 2009

Inhibition Of Lentivirus Replication By Aqueous Extracts Of Prunella Vulgaris, Melinda A. Brindley, Mark P. Widrlechner, Joe-Ann Mccoy, Patricia A. Murphy, Catherine C. Hauck, Ludmila Rizshsky, Basil J. Nikolau, Wendy Maury

NCRPIS Publications and Papers

Background
Various members of the mint family have been used historically in Chinese and Native American medicine. Many of these same family members, including Prunella vulgaris, have been reported to have anti-viral activities. To further characterize the anti-lentiviral activities of P. vulgaris, water and ethanol extractions were tested for their ability to inhibit equine infectious anemia virus (EIAV) replication.

Results
Aqueous extracts contained more anti-viral activity than did ethanol extracts, displaying potent anti-lentiviral activity against virus in cell lines as well as in primary cell cultures with little to no cellular cytotoxicity. Time-of-addition studies demonstrated that the extracts were effective ...


Pathbinder – Text Empirics And Automatic Extraction Of Biomolecular Interactions, Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao, Eve S. Wurtele Jan 2009

Pathbinder – Text Empirics And Automatic Extraction Of Biomolecular Interactions, Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao, Eve S. Wurtele

Genetics, Development and Cell Biology Presentations, Posters and Proceedings

Motivation

The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful properties that are implicit in the text. However these properties are usually not reported in the literature explicitly. By investigating specific properties of biological text passages in this paper, we aim to facilitate an alternative strategy, the use of text empirics, to support mining of biomedical texts for biomolecular interactions. We report on our application of this approach, and also report some empirical findings about an important class of passages. These may ...


Computational And Experimental Analyses Converge To Reveal A Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity, Tianjiao Wang, Julie A. Hoy, Monica H. Lamm, Marit Nilsen-Hamilton Jan 2009

Computational And Experimental Analyses Converge To Reveal A Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity, Tianjiao Wang, Julie A. Hoy, Monica H. Lamm, Marit Nilsen-Hamilton

Chemical and Biological Engineering Publications

As short nucleic acids, aptamers in solution are believed to be structurally flexible. Consistent with this view, most aptamers examined for this property have been shown to bind their target molecules by mechanisms that can be described as "induced fit". But, it is not known to what extent this structural flexibility affects the integrity of the target - aptamer interaction. Using the malachite green aptamer (MGA) as a model system, we show that the MGA can protect its bound target, malachite green (MG), from oxidation over several days. Protection is reversed by an oligonucleotide complementary to the MGA binding pocket. Computational ...


Metabolic Profiling Of Echinacea Genotypes And A Test Of Alternative Taxonomic Treatments, Lankun Wu, Philip M. Dixon, Basil J. Nikolau, George A. Kraus, Mark P. Widrlechner, Eve S. Wurtele Jan 2009

Metabolic Profiling Of Echinacea Genotypes And A Test Of Alternative Taxonomic Treatments, Lankun Wu, Philip M. Dixon, Basil J. Nikolau, George A. Kraus, Mark P. Widrlechner, Eve S. Wurtele

NCRPIS Publications and Papers

The genus Echinacea is used as an herbal medicine to treat a variety of ailments. To better understand its potential chemical variation, 40 Echinacea accessions encompassing broad geographical and morphological diversity were evaluated under controlled conditions. Metabolites of roots from these accessions were analyzed by HPLC-photo diode array (HPLC-PDA), GC-MS, and multivariate statistical methods. In total, 43 lipophilic metabolites, including 24 unknown compounds, were detected. Weighted principal component analysis (WPCA) and clustering analysis of the levels of these metabolites across Echinacea accessions, based on Canberra distances, allowed us to test two alternative taxonomic treatments of the genus, with the further ...


Prtad: A Database For Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu Jan 2009

Prtad: A Database For Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu

Biochemistry, Biophysics and Molecular Biology Publications

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modelling. The database is developed to host and analyse the statistical data for protein residue level 'virtual' bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily ...


Edaxadiene: A New Bioactive Diterpene From Mycobacterium Tuberculosis, Francis M. Mann, Meimei Xu, Xiaoming Chen, D. Bruce Fulton, David G. Russell, Reuben J. Peters Jan 2009

Edaxadiene: A New Bioactive Diterpene From Mycobacterium Tuberculosis, Francis M. Mann, Meimei Xu, Xiaoming Chen, D. Bruce Fulton, David G. Russell, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Mycobacterium tuberculosis remains a widespread and devastating human pathogen. Presented here is the characterization of an atypical class I diterpene cyclase from M. tuberculosis that catalyzes an unusual cyclization reaction in converting the known M. tuberculosis metabolite halimadienyl diphosphate to a further cyclized novel diterpene, which we have termed edaxadiene, as it directly inhibits maturation of the phagosomal compartment in which the bacterium is taken up during infection.


A Functional Genomics Approach To Tanshinone Biosynthesis Provides Stereochemical Insights, Wei Gao, Matthew L. Hillwig, Luqi Huang, Guanghong Cui, Xueyong Wang, Jianqiang Kong, Bin Yang, Reuben J. Peters Jan 2009

A Functional Genomics Approach To Tanshinone Biosynthesis Provides Stereochemical Insights, Wei Gao, Matthew L. Hillwig, Luqi Huang, Guanghong Cui, Xueyong Wang, Jianqiang Kong, Bin Yang, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Tanshinones are abietane-type norditerpenoid quinone natural products that are the bioactive components of the Chinese medicinal herb Salvia miltiorrhiza Bunge. The initial results from a functional genomics-based investigation of tanshinone biosynthesis, specifically the functional identification of the relevant diterpene synthases from S. miltiorrhiza, are reported. The cyclohexa-1,4-diene arrangement of the distal ring poises the resulting miltiradiene for the ensuing aromatization and hydroxylation to ferruginol suggested for tanshinone biosynthesis.


Novel Relationships Among Lampreys (Petromyzontiformes) Revealed By A Taxonomically Comprehensive Molecular Data Set, Nicholas J. Lang, Kevin J. Roe, Claude B. Renaud, Howard S. Gill, Ian C. Potter, Jörg Freyhof, Alexander M. Naseka, Philip Cochran, Hector Espinosa Pérez, Evelyn M. Habit, Bernard R. Kuhajda, David A. Neely, Yuri S. Reshetnikov, Vladimir B. Salnikov, Maria Th. Stoumboudi, Richard L. Mayden Jan 2009

Novel Relationships Among Lampreys (Petromyzontiformes) Revealed By A Taxonomically Comprehensive Molecular Data Set, Nicholas J. Lang, Kevin J. Roe, Claude B. Renaud, Howard S. Gill, Ian C. Potter, Jörg Freyhof, Alexander M. Naseka, Philip Cochran, Hector Espinosa Pérez, Evelyn M. Habit, Bernard R. Kuhajda, David A. Neely, Yuri S. Reshetnikov, Vladimir B. Salnikov, Maria Th. Stoumboudi, Richard L. Mayden

Natural Resource Ecology and Management Publications

The systematics of lampreys was investigated using complete mitochondrial cytochrome b sequences from all genera and nearly all recognized species. The families Geotriidae and Petromyzontidae are monophyletic, but the family Mordaciidae was resolved as two divergent lineages at the base of the tree. Within Petromyzontidae, the nonparasitic Lethenteron sp. S and Okkelbergia aepyptera were recognized as distinct lineages, Lethenteron morii and Lampetra zanandreai were moved to new genera, a sister species relationship was recovered between Caspiomyzon wagneri and Eudontomyzon hellenicus, and a clade was recovered inclusive of Entosphenus hubbsi and western North American Lampetra (L. ayresii and L. richardsoni). The ...


An Affinity-Based Scoring Scheme For Predicting Dna-Binding Activities Of Modularly Assembled Zinc-Finger Proteins, Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena L. Dobbs Jan 2009

An Affinity-Based Scoring Scheme For Predicting Dna-Binding Activities Of Modularly Assembled Zinc-Finger Proteins, Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena L. Dobbs

Genetics, Development and Cell Biology Publications

Zinc-finger proteins (ZFPs) have long been recognized for their potential to manipulate genetic information because they can be engineered to bind novel DNA targets. Individual zinc-finger domains (ZFDs) bind specific DNA triplet sequences; their apparent modularity has led some groups to propose methods that allow virtually any desired DNA motif to be targeted in vitro. In practice, however, ZFPs engineered using this ‘modular assembly’ approach do not always function well in vivo. Here we report a modular assembly scoring strategy that both identifies combinations of modules least likely to function efficientlyin vivo and provides accurate estimates of their relative ...