scholarly journals Exploring amino acid functions in a deep mutational landscape

2020 ◽  
Author(s):  
Alistair Dunham ◽  
Pedro Beltrao
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Clustering Analysis ◽  
Chemical Properties ◽  
Diverse Range ◽  
Mutational Landscape ◽  
Charged Amino Acids ◽  
Large Numbers ◽  
Recent Developments ◽  
And Chemical Properties

AbstractAmino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form disulphide or hydrogen bonds in different circumstances and charged amino acids do not always make use of their charge. The repertoire of amino acid functions and the frequency at which they occur in proteins remains understudied. Measuring large numbers of mutational consequences, which can elucidate the role an amino acid plays, was prohibitively time consuming until recent developments in deep mutational scanning. In this study we gathered data from 28 deep mutational scanning studies, covering 6291 positions in 30 proteins, and used the consequences of mutation at each position to define a mutational landscape. We demonstrated rich relationships between this landscape and biophysical or evolutionary properties. Finally, we identified 100 functional amino acid subtypes with a data-driven clustering analysis and studied their features, including their frequencies and chemical properties such as tolerating polarity, hydrophobicity or being intolerant of charge or specific amino acids. The mutational landscape and amino acid subtypes provide a foundational catalogue of amino acid functional diversity, which will be refined as the number of studied protein positions increases.

INFLUENCE OF TECHNOLOGICAL METHODS ON AMINO ACID COMPOSITION OF WHITE TABLE WINE MATERIALS

2020 ◽  
Author(s):  
А.А. Алексеева ◽  
Н.М. Агеева ◽  
В.Е. Струкова ◽  
М.А. Назаренко ◽  
Е.Н. Гонтарева
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Chemical Properties ◽  
White Wine ◽  
Tyrosine Concentration ◽  
Proline Concentration ◽  
Technological Methods ◽  
And Chemical Properties

Исследован аминокислотный состав столового сухого белого виноматериала Пино Блан, полученного сбраживанием виноградного сусла расой активных дрожжей штамма WT-1 (Германия) с последующей выдержкой молодого виноматериала на дрожжевой гуще в течение 30 сут. Установлено, что в анализируемом виноматериале доминирует пролин (422 мг/дм3). Количество аминокислот аланина и аспарагина составило 67,2 и 57,6 мг/дм3 тирозина и серина 18,4 и 17,7 мг/дм3 метионина и изолейцина 16,2 и 14,4 мг/дм3 соответственно. Глутаминовой кислоты содержится в 3 раза меньше пролина. Оклейка молодого виноматериала привела к снижению концентрации аминокислот независимо от строения и химических свойств: глицина в 3,5 раза аланина, изолейцина, серина, фенилаланина, гистидина от 2,0 до 2,7 раза аспарагина, валина, треонина, тирозина, лизина, цистина и цистеина от 1,3 до 1,9 раза. Концентрация пролина снизилась незначительно c 422 до 389 мг/дм3. После выдержки молодого виноматериала на дрожжевой гуще в течение 1 мес. концентрация большинства аминокислот не повысилась. Обработка виноматериала бентонитом привела к дальнейшему снижению концентрации аминокислот в 1,52,0 раза. Отмечено уменьшение в 1,72 раза количества цистина и цистеина, обусловливающих формирование мышиного тона в виноматериалах. В 1,57 раза снизилась концентрация тирозина в 2,7 и 2,3 раза гистидина и серина соответственно. Проведенное исследование будет способствовать дальнейшим работам по стабилизации концентрации основных аминокислот в виноматериалах. The amino acid composition of table dry white wine material Pinot Blanc was studied, obtained by fermentation of grape must with a race of active yeast strain WT-1 (Germany), followed by exposure of the young wine material to yeast for 30 days. It was established that proline (422 mg/dm3) prevails in the analyzed wine material. The number of amino acids of alanine and asparagine was 67,2 and 57,6 mg/dm3 tyrosine and serine 18,4 and 17,7 mg/dm3 methionine and isoleucine 16,2 and 14,4 mg/dm3, respectively. Glutamic acid is 3 times less than proline. Pasting of young wine material led to a decrease in the concentration of amino acids, regardless of structure and chemical properties: glycine by 3,5 times alanine, isoleucine, serine, phenylalanine, histidine from 2,0 to 2,7 times asparagine, valine, threonine, tyrosine, lysine, cystine and cysteine from 1,3 to 1,9 times. The proline concentration decreased slightly from 422 to 389 mg/dm3. After aging the young wine material on yeast for 1 month, the concentration of most amino acids did not increase. Processing of wine material with bentonite led to a further decrease in the concentration of amino acids by 1,52,0 times. There was a 1,72-fold decrease in the amount of cystine and cysteine. The tyrosine concentration decreased 1,57 times 2,7 and 2,3 times histidine and serine, respectively. The study will contribute to further work on stabilizing the concentration of basic amino acids in wine materials.

Recent developments in the utility of saturated azaheterocycles in peptidomimetics

2022 ◽  
Author(s):  
Manish Kumar Singh ◽  
Mahesh K Lakshman
Keyword(s):  
Chemical Properties ◽  
Physical And Chemical Properties ◽  
Recent Developments ◽  
Physical And Chemical ◽  
And Chemical Properties

To large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules...

scholarly journals Charged Amino Acids Conserved in the Aromatic Acid/H+ Symporter Family of Permeases Are Required for 4-Hydroxybenzoate Transport by PcaK from Pseudomonas putida

2002 ◽  
Vol 184 (5) ◽  
pp. 1444-1448 ◽  
Author(s):  
Jayna L. Ditty ◽  
Caroline S. Harwood
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Pseudomonas Putida ◽  
Essential Amino Acid ◽  
Major Facilitator Superfamily ◽  
Aromatic Acid ◽  
Transmembrane Segment ◽  
Amino Acid Motif ◽  
Charged Amino Acids ◽  
Major Facilitator

ABSTRACT Charged amino acids in the predicted transmembrane portion of PcaK, a permease from Pseudomonas putida that transports 4-hydroxybenzoate (4-HBA), were required for 4-HBA transport, and they were also required for P. putida to have a chemotactic response to 4-HBA. An essential amino acid motif (DGXD) containing aspartate residues is located in the first transmembrane segment of PcaK and is conserved in the aromatic acid/H+ symporter family of the major facilitator superfamily of transporters.

scholarly journals Porin from Marine Bacterium Marinomonas primoryensis KMM 3633T: Isolation, Physico-Chemical Properties, and Functional Activity

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3131
Author(s):  
Olga D. Novikova ◽  
Valentina A. Khomenko ◽  
Natalia Yu. Kim ◽  
Galina N. Likhatskaya ◽  
Lyudmila A. Romanenko ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Lipid Membranes ◽  
Marine Bacterium ◽  
Chemical Properties ◽  
Cell Permeability ◽  
Oligomeric Structure ◽  
Black Lipid Membranes ◽  
Physico Chemical ◽  
Coastal Sea

Marinomonas primoryensis KMM 3633T, extreme living marine bacterium was isolated from a sample of coastal sea ice in the Amursky Bay near Vladivostok, Russia. The goal of our investigation is to study outer membrane channels determining cell permeability. Porin from M. primoryensis KMM 3633T (MpOmp) has been isolated and characterized. Amino acid analysis and whole genome sequencing were the sources of amino acid data of porin, identified as Porin_4 according to the conservative domain searching. The amino acid composition of MpOmp distinguished by high content of acidic amino acids and low content of sulfur-containing amino acids, but there are no tryptophan residues in its molecule. The native MpOmp existed as a trimer. The reconstitution of MpOmp into black lipid membranes demonstrated its ability to form ion channels whose conductivity depends on the electrolyte concentration. The spatial structure of MpOmp had features typical for the classical gram-negative porins. However, the oligomeric structure of isolated MpOmp was distinguished by very low stability: heat-modified monomer was already observed at 30 °C. The data obtained suggest the stabilizing role of lipids in the natural membrane of marine bacteria in the formation of the oligomeric structure of porin.

scholarly journals The Neutral Envelopes of Planetary Nebulae: Molecules and H I

1993 ◽  
Vol 155 ◽  
pp. 147-154 ◽  
Author(s):  
P.J. Huggins
Keyword(s):  
Chemical Properties ◽  
Planetary Nebulae ◽  
Physical And Chemical Properties ◽  
Agb Stars ◽  
Subsequent Evolution ◽  
Neutral Gas ◽  
Recent Developments ◽  
Molecular Lines ◽  
Physical And Chemical ◽  
And Chemical Properties

This paper summarizes recent developments in the study of planetary nebulae using observations of molecular lines and the 21 cm line of H I. The observations reveal that many planetary nebulae are surrounded by envelopes of neutral gas, whose mass often exceeds that of the ionized nebulae. They also provide valuable information on the physical and chemical properties of the envelopes, their structure, and kinematics. The neutral envelopes firmly link the formation of planetary nebulae with the mass loss by AGB stars, and can play an important role in the subsequent evolution of the nebulae.

scholarly journals β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Marietta John-White ◽  
James Gardiner ◽  
Priscilla Johanesen ◽  
Dena Lyras ◽  
Geoffrey Dumsday
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gram Negative Bacteria ◽  
Diverse Range ◽  
Α Subunit ◽  
Gram Negative ◽  
Content Type ◽  
Proteolytic Resistance ◽  
Insight Into ◽  
Unique Capability

ABSTRACT β-Aminopeptidases have the unique capability to hydrolyze N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date, six β-aminopeptidases have been discovered and functionally characterized, five from Gram-negative bacteria and one from a fungus, Aspergillus. Here we report on the purification and characterization of an additional four β-aminopeptidases, one from a Gram-positive bacterium, Mycolicibacterium smegmatis (BapAMs), one from a yeast, Yarrowia lipolytica (BapAYlip), and two from Gram-negative bacteria isolated from activated sludge identified as Burkholderia spp. (BapABcA5 and BapABcC1). The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli, and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated, as the active enzyme was recovered after immobilized-metal affinity chromatography (IMAC) purification, even though only the α-subunit was 6-histidine tagged. The enzymes were shown to hydrolyze chromogenic substrates with the N-terminal l-configurations β-homo-Gly (βhGly) and β3-homo-Leu (β3hLeu) with high activities. These enzymes displayed higher activity with H-βhGly-p-nitroanilide (H-βhGly-pNA) than previously characterized enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions. IMPORTANCE β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilize synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterized with preferences for different β-amino acid substrates and have demonstrated the capability to catalyze not only the degradation of synthetic β-peptides but also the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with differing β-amino acid substrate preferences and kinetics. These enzymes have the potential to be utilized in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important, because β-amino acids and β-peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature.

scholarly journals Recent Developments towards Commercialization of Metal Matrix Composites

Materials ◽  
2020 ◽  
Vol 13 (12) ◽  
pp. 2828
Author(s):  
Dae-Young Kim ◽  
Hyun-Joo Choi
Keyword(s):  
Metal Matrix Composites ◽  
Metal Matrix ◽  
Chemical Properties ◽  
High Strength ◽  
Electronic Energy ◽  
Matrix Composites ◽  
Wide Range ◽  
Recent Developments ◽  
Processing Material ◽  
And Chemical Properties

Metal matrix composites (MMCs) are promising alternatives to metallic alloys. Their high strength-to-weight ratios; high temperature stabilities; and unique thermal, electrical, and chemical properties make them suitable for automotive, aerospace, defense, electrical, electronic, energy, biomedical, and other applications. The wide range of potential combinations of materials allows the properties of MMCs to be tailored by manipulating the morphology, size, orientation, and fraction of reinforcement, offering further opportunities for a variety of applications in daily life. This Special Issue, “Metal Matrix Composites”, addresses advances in the material science, processing, material modeling and characterization, performance, and testing of metal matrix composites.

Self-healing hydrogels triggered by amino acids

2016 ◽  
Vol 3 (12) ◽  
pp. 1699-1704 ◽  
Author(s):  
Nicola Zanna ◽  
Andrea Merlettini ◽  
Claudia Tomasini
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Chemical Properties ◽  
Aromatic Amino Acids ◽  
Self Healing ◽  
Acidic Amino Acid ◽  
Basic Amino Acids

Nine amino acids with different chemical properties have been chosen to promote the formation of hydrogels based on the bolamphiphilic gelator A: three basic amino acids (arginine, histidine and lysine), one acidic amino acid (aspartic acid), two neutral aliphatic amino acids (alanine and serine) and three neutral aromatic amino acids (phenylalanine, tyrosine and tryptophan).

Sign in / Sign up

Export Citation Format

Share Document