scholarly journals The meaning of biological information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150065 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Entire Range ◽  
Evolutionary Conservation ◽  
Amino Acid Sequences ◽  
Biological Information ◽  
Biological Functions ◽  
Biologically Relevant ◽  
Functional Roles ◽  
Biological Meaning ◽  
Concept Of Information ◽  
Single Sequence

Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

scholarly journals HomoKinase: A Curated Database of Human Protein Kinases

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Suresh Subramani ◽  
Saranya Jayapalan ◽  
Raja Kalpana ◽  
Jeyakumar Natarajan
Keyword(s):  
Gene Ontology ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Query Protein ◽  
Amino Acid Sequences ◽  
Human Protein ◽  
Biological Information ◽  
Functional Domain ◽  
Comprehensive Collection ◽  
Search Tool

HomoKinase database is a comprehensive collection of curated human protein kinases and their relevant biological information. The entries in the database are curated by three criteria: HGNC approval, gene ontology-based biological process (protein phosphorylation), and molecular function (ATP binding and kinase activity). For a given query protein kinase name, the database provides its official symbol, full name, other known aliases, amino acid sequences, functional domain, gene ontology, pathways assignments, and drug compounds. In addition, as a search tool, it enables the retrieval of similar protein kinases with specific family, subfamily, group, and domain combinations and tabulates the information. The present version contains 498 curated human protein kinases and links to other popular databases.

Insights into biological functions across species: examining the role of Rab proteins in YIP1 family function

2005 ◽  
Vol 33 (4) ◽  
pp. 614-618 ◽  
Author(s):  
C.Z. Chen ◽  
R.N. Collins
Keyword(s):  
Membrane Proteins ◽  
Protein Function ◽  
Evolutionary Conservation ◽  
Biological Role ◽  
Rab Proteins ◽  
Biological Functions ◽  
Human Homologue ◽  
Family Function ◽  
Evolutionarily Conserved

The YIP1 family comprises an evolutionarily conserved group of membrane proteins, which share the ability to bind di-prenylated Rab proteins. The biochemical capability of YIP1 family proteins suggests a possible role in the cycle of physical localization of Rab proteins between their cognate membranes and the cytosol. YIP1 is essential for viability in yeast and a deletion of YIP1 can be rescued with the human homologue YIP1A. We have made use of this evolutionary conservation of function to generate a series of mutant alleles of YIP1 to investigate the biological role of Yip1p. Our findings indicate evidence for the participation of Yip1p in both Rab and COPII protein function; at present, we are not able to distinguish between the models that these roles represent, i.e. independent or dependent activities of Yip1p.

scholarly journals Biological information

2020 ◽  
Vol 139 (4) ◽  
pp. 361-370
Author(s):  
Jürgen Jost
Keyword(s):  
Computer Science ◽  
Genetic Information ◽  
Spatial Organization ◽  
Environmental Information ◽  
External Factors ◽  
Biological Information ◽  
Cellular Processes ◽  
Theory Of Information ◽  
Concept Of Information

AbstractIn computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon’s concept of information is useful in biology, although its application is not as straightforward as many people think. In fact, the recently developed theory of information decomposition can shed much light on the complementarity between coding and regulatory, or internal and environmental information. The key challenge that we formulate in this contribution is to understand how genetic information and external factors combine to create an organism, and conversely how the genome has learned in the course of evolution how to harness the environment, and analogously how coding, regulation and spatial organization interact in cellular processes.

NOT THAT RIGID MIDGETS AND NOT SO FLEXIBLE GIANTS: ON THE ABUNDANCE AND ROLES OF INTRINSIC DISORDER IN SHORT AND LONG PROTEINS

2012 ◽  
Vol 20 (04) ◽  
pp. 471-511 ◽  
Author(s):  
MARK HOWELL ◽  
RYAN GREEN ◽  
ALEXIS KILLEEN ◽  
LAMAR WEDDERBURN ◽  
VINCENT PICASCIO ◽  
...  
Keyword(s):  
Amino Acid ◽  
Intrinsically Disordered Proteins ◽  
Biological Activities ◽  
Intrinsic Disorder ◽  
Amino Acid Sequences ◽  
Disordered Proteins ◽  
Biological Functions ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteins ◽  
Disordered Regions

Intrinsically disordered proteins or proteins with disordered regions are very common in nature. These proteins have numerous biological functions which are complementary to the biological activities of traditional ordered proteins. A noticeable difference in the amino acid sequences encoding long and short disordered regions was found and this difference was used in the development of length-dependent predictors of intrinsic disorder. In this study, we analyze the scaling of intrinsic disorder in eukaryotic proteins and investigate the presence of length-dependent functions attributed to proteins containing long disordered regions.

Plant natural products: a primerThe present review is one in the special series of reviews on animal–plant interactions.

2010 ◽  
Vol 88 (7) ◽  
pp. 601-614 ◽  
Author(s):  
M. A. Bernards
Keyword(s):  
Natural Products ◽  
Structural Diversity ◽  
Structural Type ◽  
Biological Functions ◽  
Plant Interactions ◽  
In Planta ◽  
Functional Roles ◽  
Chemical Mechanisms ◽  
Know How ◽  
Plant Natural Products

Over the course of evolution, plants have adapted various structural and chemical mechanisms to protect themselves and interact with their environment. The chemical mechanisms are largely based on the secondary metabolites or natural products. Although plant natural products are generally divided into three main categories (terpenoids, alkaloids, and phenylpropanoids) that are based on structural type and biosynthetic origin, there are many other smaller categories of unique compounds. Many important in planta biological functions can be attributed to plant natural products, in large part, owing to their tremendous structural diversity. To understand the functional roles of plant natural products, both as protective compounds and interorganismal signals, it is important to know how they are formed in plants. This minireview provides a general background about the three main categories of plant natural products, their biosynthetic origins, and their structural diversity.

scholarly journals Impact of the Olig Family on Neurodevelopmental Disorders

2021 ◽  
Vol 15 ◽  
Author(s):  
Jenny Szu ◽  
Alexandre Wojcinski ◽  
Peng Jiang ◽  
Santosh Kesari
Keyword(s):  
Autism Spectrum Disorder ◽  
Neurodevelopmental Disorders ◽  
Autism Spectrum ◽  
Biological Functions ◽  
Functional Roles ◽  
Neurodevelopmental Disease ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Disease States ◽  
And Function

The Olig genes encode members of the basic helix-loop-helix (bHLH) family of transcription factors. Olig1, Olig2, and Olig3 are expressed in both the developing and mature central nervous system (CNS) and strictly regulate cellular specification and differentiation. Extensive studies have established functional roles of Olig1 and Olig2 in directing neuronal and glial formation during different stages in development. Recently, Olig2 overexpression was implicated in neurodevelopmental disorders down syndrome (DS) and autism spectrum disorder (ASD) but its influence on cognitive and intellectual defects remains unknown. In this review, we summarize the biological functions of the Olig family and how it uniquely promotes cellular diversity in the CNS. This is followed up with a discussion on how abnormal Olig2 expression impacts brain development and function in DS and ASD. Collectively, the studies described here emphasize vital features of the Olig members and their distinctive potential roles in neurodevelopmental disease states.

scholarly journals Biological functions and theranostic potential of HMGB family members in human cancers

2020 ◽  
Vol 12 ◽  
pp. 175883592097085
Author(s):  
Liaoran Niu ◽  
Wanli Yang ◽  
Lili Duan ◽  
Xiaoqian Wang ◽  
Yiding Li ◽  
...  
Keyword(s):  
Malignant Tumors ◽  
Family Members ◽  
High Mobility ◽  
Amino Acid Sequences ◽  
Biological Functions ◽  
Fundamental Function ◽  
Cellular Processes ◽  
Functional Regions ◽  
Therapeutic Value ◽  
Similar Amino Acid

The high mobility group box (HMGB) protein family consists of four members: HMGB1, 2, 3, and 4. They share similar amino acid sequences and identical functional regions, especially HMGB1, 2, and 3. The homology in structure may lead to similarity in function. In fact, though their targets may be different, they all possess the fundamental function of binding and distorting target DNAs. However, further research confirmed they are distributed differently in tissues and involved in various distinct physiological and pathological cellular processes, including cell proliferation, division, migration, and differentiation. Recently, the roles of HMGB family members in carcinogenesis has been widely investigated; however, systematic discussion on their functions and clinical values in malignant tumors is limited. In this review, we mainly review and summarize recent advances in knowledge of HMGB family members in terms of structure, distribution, biochemical cascades, and specific mechanisms regarding tumor progression. Importantly, the diagnostic, prognostic, and therapeutic value of these proteins in cancers is discussed. Finally, we envisage the orientation and challenges of this field in further studies.

EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 689-691 ◽  
Author(s):  
Yoon-Seong Jeon ◽  
Kihyun Lee ◽  
Sang-Cheol Park ◽  
Bong-Soo Kim ◽  
Yong-Joon Cho ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Relevant Information ◽  
Biological Information ◽  
Sequence Alignments ◽  
Protein Coding ◽  
Structure Information ◽  
Biologically Relevant ◽  
Molecular Sequence ◽  
Protein Coding Genes

EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-generated multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionalities for editing rRNA alignments using secondary structure information. In addition, it supports simultaneous editing of both DNA sequences and their translated protein sequences for protein-coding genes. EzEditor is, to our knowledge, the first sequence editing software designed for both rRNA- and protein-coding genes with the visualization of biologically relevant information and should be useful in molecular phylogenetic studies. EzEditor is based on Java, can be run on all major computer operating systems and is freely available from http://sw.ezbiocloud.net/ezeditor/.

scholarly journals Biological Mechanisms of S-Nitrosothiol Formation and Degradation: How Is Specificity of S-Nitrosylation Achieved?

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1111
Author(s):  
Christopher M. Massa ◽  
Ziping Liu ◽  
Sheryse Taylor ◽  
Ashley P. Pettit ◽  
Marena N. Stakheyeva ◽  
...  
Keyword(s):  
Reaction Mechanisms ◽  
Chemical Nature ◽  
Biological Chemistry ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Biological Mechanisms ◽  
Radical Intermediate ◽  
Biologically Relevant ◽  
The Impact

The modification of protein cysteine residues underlies some of the diverse biological functions of nitric oxide (NO) in physiology and disease. The formation of stable nitrosothiols occurs under biologically relevant conditions and time scales. However, the factors that determine the selective nature of this modification remain poorly understood, making it difficult to predict thiol targets and thus construct informatics networks. In this review, the biological chemistry of NO will be considered within the context of nitrosothiol formation and degradation whilst considering how specificity is achieved in this important post-translational modification. Since nitrosothiol formation requires a formal one-electron oxidation, a classification of reaction mechanisms is proposed regarding which species undergoes electron abstraction: NO, thiol or S-NO radical intermediate. Relevant kinetic, thermodynamic and mechanistic considerations will be examined and the impact of sources of NO and the chemical nature of potential reaction targets is also discussed.

scholarly journals Three-Finger Toxins from Brazilian Coral Snakes: From Molecular Framework to Insights in Biological Function

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 328
Author(s):  
Jessica Matos Kleiz-Ferreira ◽  
Nuria Cirauqui ◽  
Edson Araujo Trajano ◽  
Marcius da Silva Almeida ◽  
Russolina Benedeta Zingali
Keyword(s):  
Structural Model ◽  
Biological Function ◽  
Amino Acid Sequences ◽  
Biological Functions ◽  
Future Studies ◽  
Specific Guideline ◽  
Broad Variety ◽  
And Function ◽  
Structural Homologue ◽  
Molecular Framework

Studies on 3FTxs around the world are showing the amazing diversity in these proteins both in structure and function. In Brazil, we have not realized the broad variety of their amino acid sequences and probable diversified structures and targets. In this context, this work aims to conduct an in silico systematic study on available 3FTxs found in Micrurus species from Brazil. We elaborated a specific guideline for this toxin family. First, we grouped them according to their structural homologue predicted by HHPred server and further curated manually. For each group, we selected one sequence and constructed a representative structural model. By looking at conserved features and comparing with the information available in the literature for this toxin family, we managed to point to potential biological functions. In parallel, the phylogenetic relationship was estimated for our database by maximum likelihood analyses and a phylogenetic tree was constructed including the homologous 3FTx previously characterized. Our results highlighted an astonishing diversity inside this family of toxins, showing some groups with expected functional similarities to known 3FTxs, and pointing out others with potential novel roles and perhaps structures. Moreover, this classification guideline may be useful to aid future studies on these abundant toxins.

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