Rationalising pKa shifts in Bacillus circulans xylanase with computational studies

2016 ◽  
Vol 18 (44) ◽  
pp. 30305-30312 ◽  
Author(s):  
Kela Xiao ◽  
Haibo Yu
Keyword(s):  
Molecular Mechanism ◽  
Computational Methods ◽  
Bacillus Circulans ◽  
Computational Studies ◽  
Wild Type ◽  
Pka Shifts ◽  
Bacillus Circulans Xylanase ◽  
Key Residues

Molecular mechanism for pKa shifts for the key residues in wild-type and mutants of BcX based on three different computational methods.

scholarly journals The ham-2 Locus, Encoding a Putative Transmembrane Protein, Is Required for Hyphal Fusion in Neurospora crassa

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 169-180
Author(s):  
Qijun Xiang ◽  
Carolyn Rasmussen ◽  
N Louise Glass
Keyword(s):  
Neurospora Crassa ◽  
Somatic Cell ◽  
Molecular Mechanism ◽  
Cell Fusion ◽  
Deletion Mutant ◽  
Transmembrane Protein ◽  
Wild Type ◽  
Vegetative Incompatibility ◽  
Hyphal Fusion ◽  
Aerial Hyphae

Abstract Somatic cell fusion is common during organogenesis in multicellular eukaryotes, although the molecular mechanism of cell fusion is poorly understood. In filamentous fungi, somatic cell fusion occurs during vegetative growth. Filamentous fungi grow as multinucleate hyphal tubes that undergo frequent hyphal fusion (anastomosis) during colony expansion, resulting in the formation of a hyphal network. The molecular mechanism of the hyphal fusion process and the role of networked hyphae in the growth and development of these organisms are unexplored questions. We use the filamentous fungus Neurospora crassa as a model to study the molecular mechanism of hyphal fusion. In this study, we identified a deletion mutant that was restricted in its ability to undergo both self-hyphal fusion and fusion with a different individual to form a heterokaryon. This deletion mutant displayed pleiotropic defects, including shortened aerial hyphae, altered conidiation pattern, female sterility, slow growth rate, lack of hyphal fusion, and suppression of vegetative incompatibility. Complementation with a single open reading frame (ORF) within the deletion region in this mutant restored near wild-type growth rates, female fertility, aerial hyphae formation, and hyphal fusion, but not vegetative incompatibility and wild-type conidiation pattern. This ORF, which we named ham-2 (for hyphal anastomosis), encodes a putative transmembrane protein that is highly conserved, but of unknown function among eukaryotes.

scholarly journals Intragenic suppression among CDC34 (UBC3) mutations defines a class of ubiquitin-conjugating catalytic domains.

1995 ◽  
Vol 15 (10) ◽  
pp. 5635-5644 ◽  
Author(s):  
Y Liu ◽  
N Mathias ◽  
C N Steussy ◽  
M G Goebl
Keyword(s):  
Temperature Sensitive ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Cloning And Sequencing ◽  
Mutant Proteins ◽  
Catalytic Domains ◽  
Conserved Regions ◽  
E2 Enzymes ◽  
Key Residues

Ubiquitin-conjugating (E2) enzymes contain several regions within their catalytic domains that are highly conserved. However, within some of these conserved regions are several residues that may be used to define different classes of catalytic domains for the E2 enzymes. One class can be defined by the Ubc1 protein, which contains K-65, D-90, and D-120, while the corresponding positions within the Cdc34 (Ubc3) protein, which defines a second class of enzymes, contain S-73, S-97, and S-139, respectively. The presence of these differences within otherwise highly conserved regions of this family suggests that these residues may be critical for the specificity of Cdc34 function or regulation. Therefore, we have constructed a series of cdc34 alleles encoding mutant proteins in which these serine residues have been changed to other amino acid residues, including alanine and aspartic acid. In vivo complementation studies showed that S-97, which lies near the active site C-95, is essential for Cdc34 function. The addition of a second mutation in CDC34, which now encoded both the S97D and S73K changes, restored partial function to the Cdc34 enzyme. Moreover, the deletion of residues 103 to 114 within Cdc34, which are not present in the Ubc1-like E2s, allowed the S73K/S97D mutant to function as efficiently as wild-type Cdc34 protein. Finally, the cloning and sequencing of the temperature-sensitive alleles of CDC34 indicated that A-62 is also unique to the Cdc34 class of E2 enzymes and that mutations at this position can be detrimental to Cdc34 function. Our results suggest that several key residues within conserved regions of the E2 enzyme family genetically interact with each other and define a class of E2 catalytic domains.

scholarly journals Computational studies into urea formation in the interstellar medium

2020 ◽  
Vol 497 (4) ◽  
pp. 5413-5420
Author(s):  
Eren C S Slate ◽  
Rory Barker ◽  
Ryan T Euesden ◽  
Max R Revels ◽  
Anthony J H M Meijer
Keyword(s):  
Interstellar Medium ◽  
Computational Methods ◽  
Radical Reaction ◽  
Closed Shell ◽  
Computational Studies ◽  
Water Ice ◽  
Charged Species ◽  
Ice Shell ◽  
Partial Water

ABSTRACT Formation routes, involving closed shell, radical, and charged species for urea, have been studied using computational methods to probe their feasibility in the interstellar medium. All reactions involving closed shell species were found to have prohibitive barriers. The radical–radical reaction possesses a barrier of only 4 kJ mol−1, which could be surmountable. A charged species based route was also investigated. A barrier of only 8 kJ mol−1 was found in that case, when a partial water ice shell was included.

scholarly journals Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiaofang Xie ◽  
Zhiwei Chen ◽  
Binghui Zhang ◽  
Huazhong Guan ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Cell Death ◽  
Molecular Mechanism ◽  
Oryza Sativa L ◽  
Blast Resistance ◽  
Rna Seq ◽  
Bacterial Leaf Streak ◽  
Wild Type ◽  
Cell Death Pathways ◽  
Rnai Line ◽  
Transgenic Lines

Abstract Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.

scholarly journals A microtubule-dynein tethering complex regulates the axonemal inner dynein f (I1)

2018 ◽  
Vol 29 (9) ◽  
pp. 1060-1074 ◽  
Author(s):  
Tomohiro Kubo ◽  
Yuqing Hou ◽  
Deborah A. Cochran ◽  
George B. Witman ◽  
Toshiyuki Oda
Keyword(s):  
Conformational Change ◽  
Molecular Mechanism ◽  
Wild Type ◽  
Sliding Direction ◽  
Large Conformational Change ◽  
Dynein Arms ◽  
Biochemical Analyses

Motility of cilia/flagella is generated by a coordinated activity of thousands of dyneins. Inner dynein arms (IDAs) are particularly important for the formation of ciliary/flagellar waveforms, but the molecular mechanism of IDA regulation is poorly understood. Here we show using cryoelectron tomography and biochemical analyses of Chlamydomonas flagella that a conserved protein FAP44 forms a complex that tethers IDA f (I1 dynein) head domains to the A-tubule of the axonemal outer doublet microtubule. In wild-type flagella, IDA f showed little nucleotide-dependent movement except for a tilt in the f β head perpendicular to the microtubule-sliding direction. In the absence of the tether complex, however, addition of ATP and vanadate caused a large conformational change in the IDA f head domains, suggesting that the movement of IDA f is mechanically restricted by the tether complex. Motility defects in flagella missing the tether demonstrates the importance of the IDA f-tether interaction in the regulation of ciliary/flagellar beating.

scholarly journals Combining Experimental Data and Computational Methods for the Non-Computer Specialist

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4783
Author(s):  
Reinier Cárdenas ◽  
Javier Martínez-Seoane ◽  
Carlos Amero
Keyword(s):  
Experimental Data ◽  
Molecular Mechanism ◽  
Computational Methods ◽  
Dynamic Systems ◽  
Experimental Methods ◽  
Computational Techniques ◽  
Biological Macromolecules ◽  
Basic Principles ◽  
Structural Interpretation

Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.

scholarly journals Unstable Spinocerebellar Ataxia Type 10 (ATTCT)·(AGAAT) Repeats Are Associated with Aberrant Replication at the ATX10 Locus and Replication Origin-Dependent Expansion at an Ectopic Site in Human Cells

2007 ◽  
Vol 27 (22) ◽  
pp. 7828-7838 ◽  
Author(s):  
Guoqi Liu ◽  
John J. Bissler ◽  
Richard R. Sinden ◽  
Michael Leffak
Keyword(s):  
Molecular Mechanism ◽  
Cell Lines ◽  
Spinocerebellar Ataxia ◽  
Replication Origin ◽  
Spinocerebellar Ataxia Type ◽  
Dna Unwinding ◽  
Wild Type ◽  
Normal Length ◽  
Population Doublings

ABSTRACT Spinocerebellar ataxia type 10 (SCA10) is associated with expansion of (ATTCT) n repeats (where n is the number of repeats) within the ataxin 10 (ATX10/E46L) gene. The demonstration that (ATTCT) n tracts can act as DNA unwinding elements (DUEs) in vitro has suggested that aberrant replication origin activity occurs at expanded (ATTCT) n tracts and may lead to their instability. Here, we confirm these predictions. The wild-type ATX10 locus displays inefficient origin activity, but origin activity is elevated at the expanded ATX10 loci in patient-derived cells. To test whether (ATTCT) n tracts can potentiate origin activity, cell lines were constructed that contain ectopic copies of the c-myc replicator in which the essential DUE was replaced by ATX10 DUEs with (ATTCT) n . ATX10 DUEs containing (ATTCT)27 or (ATTCT)48, but not (ATTCT)8 or (ATTCT)13, could substitute functionally for the c-myc DUE, but (ATTCT)48 could not act as an autonomous replicator. Significantly, chimeric c-myc replicators containing ATX10 DUEs displayed length-dependent (ATTCT) n instability. By 250 population doublings, dramatic two- and fourfold length expansions were observed for (ATTCT)27 and (ATTCT)48 but not for (ATTCT)8 or (ATTCT)13. These results implicate replication origin activity as one molecular mechanism associated with the instability of (ATTCT) n tracts that are longer than normal length.

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