Computational approaches for the prediction of protein function in the mitochondrion

2006 ◽  
Vol 291 (6) ◽  
pp. C1121-C1128 ◽  
Author(s):  
Toni Gabaldón
Keyword(s):  
Biological System ◽  
Protein Function ◽  
Research Field ◽  
Computational Techniques ◽  
Complex Biological System ◽  
Computational Approaches ◽  
Functional Interactions ◽  
Physical Interactions ◽  
Computational Research

Understanding a complex biological system, such as the mitochondrion, requires the identification of the complete repertoire of proteins targeted to the organelle, the characterization of these, and finally, the elucidation of the functional and physical interactions that occur within the mitochondrion. In the last decade, significant developments have contributed to increase our understanding of the mitochondrion, and among these, computational research has played a significant role. Not only general bioinformatics tools have been applied in the context of the mitochondrion, but also some computational techniques have been specifically developed to address problems that arose from within the mitochondrial research field. In this review the contribution of bioinformatics to mitochondrial biology is addressed through a survey of current computational methods that can be applied to predict which proteins will be localized to the mitochondrion and to unravel their functional interactions.

A complex biological system: the fly's visual module

2007 ◽  
Vol 366 (1864) ◽  
pp. 345-357 ◽  
Author(s):  
Murilo S Baptista ◽  
Lirio O.B de Almeida ◽  
Jan F.W Slaets ◽  
Roland Köberle ◽  
Celso Grebogi
Keyword(s):  
Probability Measure ◽  
Complex Systems ◽  
Visual System ◽  
Lyapunov Exponents ◽  
Biological System ◽  
Dimensional Space ◽  
Point Of View ◽  
Two Dimensional ◽  
Complex Biological System

Is the characterization of biological systems as complex systems in the mathematical sense a fruitful assertion? In this paper we argue in the affirmative, although obviously we do not attempt to confront all the issues raised by this question. We use the fly's visual system as an example and analyse our experimental results of one particular neuron in the fly's visual system from this point of view. We find that the motion-sensitive ‘H1’ neuron, which converts incoming signals into a sequence of identical pulses or ‘spikes’, encodes the information contained in the stimulus into an alphabet composed of a few letters. This encoding occurs on multilayered sets, one of the features attributed to complex systems . The conversion of intervals between consecutive occurrences of spikes into an alphabet requires us to construct a generating partition . This entails a one-to-one correspondence between sequences of spike intervals and words written in the alphabet. The alphabet dynamics is multifractal both with and without stimulus, though the multifractality increases with the stimulus entropy. This is in sharp contrast to models generating independent spike intervals, such as models using Poisson statistics, whose dynamics is monofractal. We embed the support of the probability measure, which describes the distribution of words written in this alphabet, in a two-dimensional space, whose topology can be reproduced by an M-shaped map. This map has positive Lyapunov exponents, indicating a chaotic-like encoding.

scholarly journals Computational characterization of moonlighting proteins

2014 ◽  
Vol 42 (6) ◽  
pp. 1780-1785 ◽  
Author(s):  
Ishita K. Khan ◽  
Daisuke Kihara
Keyword(s):  
Functional Diversity ◽  
Protein Function ◽  
Polypeptide Chain ◽  
Short Review ◽  
Cell Type ◽  
Cellular Functions ◽  
Computational Approaches ◽  
Cellular Location ◽  
Moonlighting Proteins

Moonlighting proteins perform multiple independent cellular functions within one polypeptide chain. Moonlighting proteins switch functions depending on various factors including the cell-type in which they are expressed, cellular location, oligomerization status and the binding of different ligands at different sites. Although an increasing number of moonlighting proteins have been experimentally identified in recent years, the quantity of known moonlighting proteins is insufficient to elucidate their overall landscape. Moreover, most moonlighting proteins have been identified as a serendipitous discovery. Hence, characterization of moonlighting proteins using bioinformatics approaches can have a significant impact on the overall understanding of protein function. In this work, we provide a short review of existing computational approaches for illuminating the functional diversity of moonlighting proteins.

Preparation and Characterization of β-glucosidase Films for Stabilization and Handling in Dry Configurations

2020 ◽  
Vol 21 (8) ◽  
pp. 741-747
Author(s):  
Liguang Zhang ◽  
Yanan Shen ◽  
Wenjing Lu ◽  
Lengqiu Guo ◽  
Min Xiang ◽  
...  
Keyword(s):  
Tensile Strength ◽  
Protein Function ◽  
Protein Stabilization ◽  
Functional Protein ◽  
Elongation At Break ◽  
Gelatin Films ◽  
The Stability ◽  
And Function ◽  
General Method

Background: Although the stability of proteins is of significance to maintain protein function for therapeutical applications, this remains a challenge. Herein, a general method of preserving protein stability and function was developed using gelatin films. Method: Enzymes immobilized onto films composed of gelatin and Ethylene Glycol (EG) were developed to study their ability to stabilize proteins. As a model functional protein, β-glucosidase was selected. The tensile properties, microstructure, and crystallization behavior of the gelatin films were assessed. Result: Our results indicated that film configurations can preserve the activity of β-glucosidase under rigorous conditions (75% relative humidity and 37°C for 47 days). In both control films and films containing 1.8 % β-glucosidase, tensile strength increased with increased EG content, whilst the elongation at break increased initially, then decreased over time. The presence of β-glucosidase had a negligible influence on tensile strength and elongation at break. Scanning electron-microscopy (SEM) revealed that with increasing EG content or decreasing enzyme concentrations, a denser microstructure was observed. Conclusion: In conclusion, the dry film is a promising candidate to maintain protein stabilization and handling. The configuration is convenient and cheap, and thus applicable to protein storage and transportation processes in the future.

scholarly journals Growth Promotion or Osmotic Stress Response: How SNF1-Related Protein Kinase 2 (SnRK2) Kinases Are Activated and Manage Intracellular Signaling in Plants

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1443
Author(s):  
Yoshiaki Kamiyama ◽  
Sotaro Katagiri ◽  
Taishi Umezawa
Keyword(s):  
Protein Kinase ◽  
Plant Growth ◽  
Osmotic Stress ◽  
Protein Function ◽  
Intracellular Signaling ◽  
Growth Promotion ◽  
Research Field ◽  
Dependent Manner ◽  
Related Protein ◽  
Wide Range

Reversible phosphorylation is a major mechanism for regulating protein function and controls a wide range of cellular functions including responses to external stimuli. The plant-specific SNF1-related protein kinase 2s (SnRK2s) function as central regulators of plant growth and development, as well as tolerance to multiple abiotic stresses. Although the activity of SnRK2s is tightly regulated in a phytohormone abscisic acid (ABA)-dependent manner, recent investigations have revealed that SnRK2s can be activated by group B Raf-like protein kinases independently of ABA. Furthermore, evidence is accumulating that SnRK2s modulate plant growth through regulation of target of rapamycin (TOR) signaling. Here, we summarize recent advances in knowledge of how SnRK2s mediate plant growth and osmotic stress signaling and discuss future challenges in this research field.

scholarly journals Molecular and Pharmacological Characterization of the Interaction between Human Geranylgeranyltransferase Type I and Ras-Related Protein Rap1B

2021 ◽  
Vol 22 (5) ◽  
pp. 2501
Author(s):  
Sonja Hinz ◽  
Dominik Jung ◽  
Dorota Hauert ◽  
Hagen S. Bachmann
Keyword(s):  
Protein Function ◽  
Tumor Development ◽  
Cysteine Residue ◽  
Type I ◽  
Pharmacological Characterization ◽  
Anti Cancer ◽  
And Function ◽  
Caax Motif ◽  
Important Drug

Geranylgeranyltransferase type-I (GGTase-I) represents an important drug target since it contributes to the function of many proteins that are involved in tumor development and metastasis. This led to the development of GGTase-I inhibitors as anti-cancer drugs blocking the protein function and membrane association of e.g., Rap subfamilies that are involved in cell differentiation and cell growth. In the present study, we developed a new NanoBiT assay to monitor the interaction of human GGTase-I and its substrate Rap1B. Different Rap1B prenylation-deficient mutants (C181G, C181S, and ΔCQLL) were designed and investigated for their interaction with GGTase-I. While the Rap1B mutants C181G and C181S still exhibited interaction with human GGTase-I, mutant ΔCQLL, lacking the entire CAAX motif (defined by a cysteine residue, two aliphatic residues, and the C-terminal residue), showed reduced interaction. Moreover, a specific, peptidomimetic and competitive CAAX inhibitor was able to block the interaction of Rap1B with GGTase-I. Furthermore, activation of both Gαs-coupled human adenosine receptors, A2A (A2AAR) and A2B (A2BAR), increased the interaction between GGTase-I and Rap1B, probably representing a way to modulate prenylation and function of Rap1B. Thus, A2AAR and A2BAR antagonists might be promising candidates for therapeutic intervention for different types of cancer that overexpress Rap1B. Finally, the NanoBiT assay provides a tool to investigate the pharmacology of GGTase-I inhibitors.

scholarly journals Avoided motifs: short amino acid strings missing from protein datasets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Large Protein ◽  
New Approach ◽  
Cellular Context ◽  
Human Proteins ◽  
Context Specific ◽  
Protein Datasets

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.

scholarly journals Common Phase and Structure Misidentifications in High-Resolution TEM Characterization of Perovskite Materials

2020 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Yu-Hao Deng
Keyword(s):  
High Resolution ◽  
Research Field ◽  
Structure Characterization ◽  
Phase Identification ◽  
Lead Iodide ◽  
Perovskite Materials ◽  
High Resolution Tem ◽  
Methylammonium Lead Iodide ◽  
Dose Imaging

High-resolution TEM (HRTEM) is a powerful tool for structure characterization. However, methylammonium lead iodide (MAPbI3) perovskite is highly sensitive to electron beams and easily decomposes into lead iodide (PbI2). Misidentifications, such as PbI2 being incorrectly labeled as perovskite, are widely present in HRTEM characterization and would negatively affect the development of perovskite research field. Here misidentifications in MAPbI3 perovskite are summarized, classified, and corrected based on low-dose imaging and electron diffraction (ED) simulations. Corresponding crystallographic parameters of intrinsic tetragonal MAPbI3 and the confusable hexagonal PbI2 are presented unambiguously. Finally, the method of proper phase identification and some strategies to control the radiation damage in HRTEM are provided. This warning paves the way to avoid future misinterpretations in HRTEM characterization of perovskite and other electron beam-sensitive materials.

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

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