@article{FedyuninLehnhardtBoehmeretal.2012, author = {Fedyunin, Ivan and Lehnhardt, Lothar and B{\"o}hmer, Nadine and Kaufmann, Paul and Zhang, Gong and Ignatova, Zoya}, title = {tRNA concentration fine tunes protein solubility}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {586}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {19}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2012.07.012}, pages = {3336 -- 3340}, year = {2012}, abstract = {Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coil increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.}, language = {en} } @inproceedings{FerrolinoZhuravlevaIgnatovaetal.2012, author = {Ferrolino, Mylene and Zhuravleva, Anastasia and Ignatova, Zoya and Gierasch, Lila}, title = {Exploring In vitro and in vivo aggregation of a beta-Clam protein}, series = {Protein science : a publication of the Protein Society}, volume = {21}, booktitle = {Protein science : a publication of the Protein Society}, number = {2}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0961-8368}, pages = {89 -- 89}, year = {2012}, language = {en} } @article{HinzLehnhardtZakrzewskietal.2012, author = {Hinz, Justyna and Lehnhardt, Lothar and Zakrzewski, Silke and Zhang, Gong and Ignatova, Zoya}, title = {Polyglutamine expansion alters the dynamics and molecular architecture of aggregates in dentatorubropallidoluysian atrophy}, series = {The journal of biological chemistry}, volume = {287}, journal = {The journal of biological chemistry}, number = {3}, publisher = {American Society for Biochemistry and Molecular Biology}, address = {Bethesda}, issn = {0021-9258}, doi = {10.1074/jbc.M111.318915}, pages = {2068 -- 2078}, year = {2012}, abstract = {Preferential accumulation of mutant proteins in the nucleus has been suggested to be the molecular culprit that confers cellular toxicity in the neurodegenerative disorders caused by polyglutamine (polyQ) expansion. Here, we use dynamic imaging approaches, orthogonal cross-seeding, and composition analysis to examine the dynamics and structure of nuclear and cytoplasmic inclusions of atrophin-1, implicated in dentatorubropallidoluysian atrophy, a polyQ-based disease with complex clinical features. Our results reveal a large heterogeneity in the dynamics of the nuclear inclusions compared with the compact and immobile cytoplasmic aggregates. At least two types of inclusions of expanded atrophin-1 with different mobility of the molecular species and ability to exchange with the surrounding monomer pool coexist in the nucleus. Intriguingly, the enrichment of nuclear inclusions with slow dynamics parallels changes in the aggregate core architecture that are dominated by the polyQ stretch. We propose that the observed complexity in the dynamics of the nuclear inclusions provides a molecular explanation for the enhanced cellular toxicity of the nuclear aggregates in polyQ-based neurodegeneration.}, language = {en} } @article{MiettinenKnechtMonticellietal.2012, author = {Miettinen, Markus S. and Knecht, Volker and Monticelli, Luca and Ignatova, Zoya}, title = {Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations}, series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, volume = {116}, journal = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry}, number = {34}, publisher = {American Chemical Society}, address = {Washington}, issn = {1520-6106}, doi = {10.1021/jp305065c}, pages = {10259 -- 10265}, year = {2012}, abstract = {Polyglutamine (polyQ) diseases comprise a group of dominantly inherited pathology caused by an expansion of an unstable polyQ stretch which is presumed to form beta-sheets. Similar to other amyloid pathologies, polyQ amyloidogenesis occurs via a nucleated polymerization mechanism, and proceeds through energetically unfavorable nucleus whose existence and structure are difficult to detect. Here, we use atomistic molecular dynamics simulations in explicit solvent to assess the conformation of the polyQ stretch in the nucleus that initiates polyQ fibrillization. Comparison of the kinetic stability of various structures of polyQ peptide with a Q-length in the pathological range (Q(40)) revealed that steric zipper or nanotube-like structures (beta-nanotube or beta-pseudohelix) are not kinetically stable enough to serve as a template to initiate polyQ fibrillization as opposed to beta-hairpin-based (beta-sheet and beta-sheetstack) or alpha-helical conformations. The selection of different structures of the polyQ stretch in the aggregation-initiating event may provide an alternative explanation for polyQ aggregate polymorphism.}, language = {en} } @article{VarshneyKumarIgnatovaetal.2012, author = {Varshney, Nishant Kumar and Kumar, R. Suresh and Ignatova, Zoya and Prabhune, Asmita and Pundle, Archana and Dodson, Eleanor and Suresh, C. G.}, title = {Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis}, series = {Acta crystallographica : Section F, Structural biology communications}, volume = {68}, journal = {Acta crystallographica : Section F, Structural biology communications}, number = {3}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {1744-3091}, doi = {10.1107/S1744309111053930}, pages = {273 -- 277}, year = {2012}, abstract = {The enzyme penicillin G acylase (EC 3.5.1.11) catalyzes amide-bond cleavage in benzylpenicillin (penicillin G) to yield 6-aminopenicillanic acid, an intermediate chemical used in the production of semisynthetic penicillins. A thermostable penicillin G acylase from Alcaligenes faecalis (AfPGA) has been crystallized using the hanging-drop vapour-diffusion method in two different space groups: C2221, with unit-cell parameters a = 72.9, b = 86.0, c = 260.2 angstrom, and P41212, with unit-cell parameters a = b = 85.6, c = 298.8 angstrom. Data were collected at 293 K and the structure was determined using the molecular-replacement method. Like other penicillin acylases, AfPGA belongs to the N-terminal nucleophilic hydrolase superfamily, has undergone post-translational processing and has a serine as the N-terminal residue of the beta-chain. A disulfide bridge has been identified in the structure that was not found in the other two known penicillin G acylase structures. The presence of the disulfide bridge is perceived to be one factor that confers higher stability to this enzyme.}, language = {en} } @article{ZhangFedyuninKirchneretal.2012, author = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya}, title = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads}, series = {Nucleic acids research}, volume = {40}, journal = {Nucleic acids research}, number = {11}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0305-1048}, doi = {10.1093/nar/gks196}, pages = {11}, year = {2012}, abstract = {The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.}, language = {en} }