scholarly journals In situFTIR Assessment of Desiccation-Tolerant Tissues

2003 ◽  
Vol 17 (2-3) ◽  
pp. 297-313 ◽  
Author(s):  
Willem F. Wolkers ◽  
Folkert A. Hoekstra
Keyword(s):  
Secondary Structure ◽  
Desiccation Tolerance ◽  
Higher Plants ◽  
Protein Secondary Structure ◽  
Biological Tissues ◽  
Glassy Matrix ◽  
Vibration Band ◽  
Helical Structures ◽  
Ftir Studies ◽  
Stretching Vibration

This essay shows how Fourier transform infrared (FTIR) microspectroscopy can be applied to study thermodynamic parameters and conformation of endogenous biomolecules in desiccation-tolerant biological tissues. Desiccation tolerance is the remarkable ability of some organisms to survive complete dehydration. Seed and pollen of higher plants are well known examples of desiccation-tolerant tissues. FTIR studies on the overall protein secondary structure indicate that during the acquisition of desiccation tolerance, plant embryos exhibit proportional increases inα-helical structures and thatµ-sheet structures dominate upon drying of desiccation sensitive-embryos. During ageing of pollen and seeds, the overall protein secondary structure remains stable, whereas drastic changes in the thermotropic response of membranes occur, which coincide with a complete loss of viability. Properties of the cytoplasmic glassy matrix in desiccation-tolerant plant organs can be studied by monitoring the position of the OH-stretching vibration band of endogenous carbohydrates and proteins as a function of temperature. By applying these FTIR techniques to maturation-defective mutant seeds ofArabidopsis thalianawe were able to establish a correlation between macromolecular stability and desiccation tolerance. Taken together,in situFTIR studies can give unique information on conformation and stability of endogenous biomolecules in desiccation-tolerant tissues.

scholarly journals The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 20
Author(s):  
Angel J. Matilla
Keyword(s):  
Desiccation Tolerance ◽  
Molecular Mechanisms ◽  
Higher Plants ◽  
Soluble Sugars ◽  
Late Embryogenesis Abundant ◽  
Seed Maturation ◽  
Glassy Matrix ◽  
Cellular Protection ◽  
Living Entity ◽  
Orthodox Seeds

To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular “glass state”. This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.

scholarly journals Helical structure motifs made searchable for functional peptide design

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Cheng-Yu Tsai ◽  
Emmanuel Oluwatobi Salawu ◽  
Hongchun Li ◽  
Guan-Yu Lin ◽  
Ting-Yu Kuo ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Point Mutations ◽  
Protein Secondary Structure ◽  
Helical Structure ◽  
Peptide Design ◽  
Sequence Motifs ◽  
Helical Structures ◽  
Protein Protein Interaction ◽  
Functional Peptides ◽  
Functional Peptide

AbstractThe systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

POSSIBILITY OF MOLECULAR-SWITCH WITH CONTROLLED HYDROGEN BOND: UTILITY OF COMBINATION OF 2,2′-BIIMIDAZOLE AND REDOX-ACTIVE LIGAND

2005 ◽  
Vol 04 (01) ◽  
pp. 333-344 ◽  
Author(s):  
HIROTOSHI MORI ◽  
EISAKU MIYOSHI
Keyword(s):  
Density Functional ◽  
Molecular Level ◽  
Molecular Switch ◽  
Vibration Band ◽  
Functional Theory ◽  
Inorganic Molecule ◽  
Redox Active Ligand ◽  
Active Ligand ◽  
Redox Active ◽  
Stretching Vibration

A new inorganic molecule [ Co(Hbim) ( C 6 H 4 O 2)( NH 3)2]2 that can be used as a new optically durable molecular switch was theoretically designed in the framework of density functional theory. Three stable minima, belonging to 1 A g , 5 A 1, and 9 A g states, were found in the complex. Theoretically predicted infrared spectra of the complexes showed that a strong peak of NH stretching vibration is observed at 2690, 2120, and 2770 cm -1 in the 1 A g , 5 A 1, and 9 A g states, respectively. The apparent red shift of the NH stretching vibration band in the 5 A 1 state make it possible to distinguish the electronic state from others (1 A g and 9 A g ). This means that the complex can be used as a molecular level switch whose memory can be stably read by IR light without any photoreaction process; namely, without memory degradation.

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