Structural and mechanistic insight into alkane hydroxylation by Pseudomonas putida AlkB

2014 ◽  
Vol 460 (2) ◽  
pp. 283-293 ◽  
Author(s):  
Hernan Alonso ◽  
Oded Kleifeld ◽  
Adva Yeheskel ◽  
Poh C. Ong ◽  
Yu C. Liu ◽  
...  
Keyword(s):  
Ab Initio ◽  
Pseudomonas Putida ◽  
Structure And Function ◽  
Alkane Hydroxylation ◽  
Mechanistic Insight ◽  
Unknown Structure ◽  
And Function ◽  
Alkane Hydroxylases ◽  
Insight Into

Integral membrane non-haem di-iron alkane hydroxylases (AlkBs) are enzymes of unknown structure that allow bacteria to grow on alkanes. Catalysis-linked modifications with the inhibitor 1-octyne, mutagenesis studies and ab initio modelling provided novel insights into the structure and function of AlkB.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Computational Approaches to Predict the Non-canonical DNAs

2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim
Keyword(s):  
Computational Methods ◽  
Genetic Instability ◽  
Computational Prediction ◽  
Structure And Function ◽  
Sequence Motifs ◽  
Computational Approaches ◽  
Functional Roles ◽  
And Function ◽  
Genetic Events ◽  
Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

scholarly journals In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1395
Author(s):  
Shahram Mesdaghi ◽  
David L. Murphy ◽  
Filomeno Sánchez Rodríguez ◽  
J. Javier Burgos-Mármol ◽  
Daniel J. Rigden
Keyword(s):  
Ab Initio ◽  
Rotational Symmetry ◽  
Domain Boundary ◽  
Pfam Domain ◽  
Transmembrane Proteins ◽  
Large Family ◽  
Data Bank ◽  
Structural Features ◽  
Structure And Function ◽  
And Function

Background: Recent strides in computational structural biology have opened up an opportunity to understand previously uncharacterised proteins.  The under-representation of transmembrane proteins in the Protein Data Bank highlights the need to apply new and advanced bioinformatics methods to shed light on their structure and function.  This study focuses on a family of transmembrane proteins containing the Pfam domain PF09335 ('SNARE_ASSOC'/ ‘VTT ‘/’Tvp38’). One prominent member, Tmem41b, has been shown to be involved in early stages of autophagosome formation and is vital in mouse embryonic development as well as being identified as a viral host factor of SARS-CoV-2. Methods: We used evolutionary covariance-derived information to construct and validate ab initio models, make domain boundary predictions and infer local structural features.  Results: The results from the structural bioinformatics analysis of Tmem41b and its homologues showed that they contain a tandem repeat that is clearly visible in evolutionary covariance data but much less so by sequence analysis.  Furthermore, cross-referencing of other prediction data with covariance analysis showed that the internal repeat features two-fold rotational symmetry.  Ab initio modelling of Tmem41b and homologues reinforces these structural predictions.  Local structural features predicted to be present in Tmem41b were also present in Cl-/H+ antiporters.  Conclusions: The results of this study strongly point to Tmem41b and its homologues being transporters for an as-yet uncharacterised substrate and possibly using H+ antiporter activity as its mechanism for transport.

scholarly journals ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 70 ◽  
Author(s):  
Espen Mikal Robertsen ◽  
Hubert Denise ◽  
Alex Mitchell ◽  
Robert D. Finn ◽  
Lars Ailo Bongo ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Genetic Material ◽  
Structure And Function ◽  
Marine Microbes ◽  
Exploration And Exploitation ◽  
Domain Specific ◽  
User Centric ◽  
Sustainable Services ◽  
And Function ◽  
Insight Into

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”.

1H, 13C and 15N resonance assignments of YajG, an Escherichia coli protein of unknown structure and function

2007 ◽  
Vol 1 (1) ◽  
pp. 89-91 ◽  
Author(s):  
Julien Boudet ◽  
Anne Chouquet ◽  
Aicha Chahboune ◽  
Cécile Giustini ◽  
Bernard Joris ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resonance Assignments ◽  
Structure And Function ◽  
Unknown Structure ◽  
And Function

Structure and function of USP5: Insight into physiological and pathophysiological roles

2020 ◽  
Vol 157 ◽  
pp. 104557 ◽  
Author(s):  
Fengling Ning ◽  
Hong Xin ◽  
Junqiu Liu ◽  
Chao Lv ◽  
Xin Xu ◽  
...  
Keyword(s):  
Structure And Function ◽  
And Function ◽  
Insight Into

scholarly journals The contribution of voltage clamp fluorometry to the understanding of channel and transporter mechanisms

2019 ◽  
Vol 151 (10) ◽  
pp. 1163-1172 ◽  
Author(s):  
John Cowgill ◽  
Baron Chanda
Keyword(s):  
Voltage Clamp ◽  
Conformational Changes ◽  
Physiological State ◽  
Structure And Function ◽  
Modern Biology ◽  
The Past ◽  
Mechanistic Insight ◽  
Atomistic Models ◽  
Multiple Conformations ◽  
And Function

Key advances in single particle cryo-EM methods in the past decade have ushered in a resolution revolution in modern biology. The structures of many ion channels and transporters that were previously recalcitrant to crystallography have now been solved. Yet, despite having atomistic models of many complexes, some in multiple conformations, it has been challenging to glean mechanistic insight from these structures. To some extent this reflects our inability to unambiguously assign a given structure to a particular physiological state. One approach that may allow us to bridge this gap between structure and function is voltage clamp fluorometry (VCF). Using this technique, dynamic conformational changes can be measured while simultaneously monitoring the functional state of the channel or transporter. Many of the important papers that have used VCF to probe the gating mechanisms of channels and transporters have been published in the Journal of General Physiology. In this review, we provide an overview of the development of VCF and discuss some of the key problems that have been addressed using this approach. We end with a brief discussion of the outlook for this technique in the era of high-resolution structures.

scholarly journals ENaC structure and function in the wake of a resolved structure of a family member

2011 ◽  
Vol 301 (4) ◽  
pp. F684-F696 ◽  
Author(s):  
Ossama B. Kashlan ◽  
Thomas R. Kleyman
Keyword(s):  
Plasma Membrane ◽  
Ion Channel ◽  
Functional Data ◽  
Ion Selectivity ◽  
External Environment ◽  
Structure And Function ◽  
Close Proximity ◽  
Channel Assembly ◽  
And Function ◽  
Insight Into

Our understanding of epithelial Na+ channel (ENaC) structure and function has been profoundly impacted by the resolved structure of the homologous acid-sensing ion channel 1 (ASIC1). The structure of the extracellular and pore regions provide insight into channel assembly, processing, and the ability of these channels to sense the external environment. The absence of intracellular structures precludes insight into important interactions with intracellular factors that regulate trafficking and function. The primary sequences of ASIC1 and ENaC subunits are well conserved within the regions that are within or in close proximity to the plasma membrane, but poorly conserved in peripheral domains that may functionally differentiate family members. This review examines functional data, including ion selectivity, gating, and amiloride block, in light of the resolved ASIC1 structure.

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