scholarly journals Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides

2020 ◽  
Author(s):  
Matthew H Zimmer ◽  
Michiel JM Niesen ◽  
Thomas F Miller
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Protein Biosynthesis ◽  
Essential Amino Acids ◽  
Structural Features ◽  
Applied Force ◽  
Catalytic Center ◽  
Force Propagation ◽  
Force Transduction

AbstractForce-sensitive arrest peptides regulate protein biosynthesis by stalling the ribosome as they are translated. Synthesis can be resumed when the nascent arrest peptide experiences a pulling force of sufficient magnitude to break the stall. Efficient stalling is dependent on the specific identity of a large number of amino acids, including amino acids which are tens of angstroms away from the peptidyl transferase center (PTC). The mechanism of force-induced restart and the role of these essential amino acids far from the PTC is currently unknown. We use hundreds of independent molecular dynamics trajectories spanning over 120 μs in combination with kinetic analysis to characterize the barriers along the force-induced restarting pathway for the arrest peptide SecM. We find that the essential amino acids far from the PTC play a major role in controlling the transduction of applied force. In successive states along the stall-breaking pathway, the applied force propagates up the nascent chain until it reaches the C-terminus of SecM and the PTC, inducing conformational changes that allow for restart of translation. A similar mechanism of force propagation through multiple states is observed in the VemP stall-breaking pathway, but secondary structure in VemP allows for heterogeneity in the order of transitions through intermediate states. Results from both arrest peptides explain how residues that are tens of angstroms away from the catalytic center of the ribosome impact stalling efficiency by mediating the response to an applied force and shielding the amino acids responsible for maintaining the stalled state of the PTC.Significance StatementAs nascent proteins are synthesized by the ribosome, their interactions with the environment can create pulling forces on the nascent protein that can be transmitted to the ribosome’s catalytic center. These forces can affect the rate and even the outcome of translation. We use simulations to characterize the pathway of force transduction along arrest peptides and discover how secondary structure in the nascent protein and its interactions with the ribosome exit tunnel impede force propagation. This explains how amino acids in arrest peptides that are tens of angstroms away from the ribosome’s catalytic center contribute to stalling, and, more broadly, suggests how structural features in the nascent protein dictate the ribosome’s ability to functionally respond to its environment.

MATHEMATICAL MODELS FOR THE SYNTHESIS OF PLANT-BASED COMPOSITIONS WITH IMPROVED AMINO ACID COMPOSITION

2021 ◽  
Author(s):  
Irina Gaivoronskaya ◽  
Valenitna Kolpakova
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mathematical Models ◽  
Functional Properties ◽  
Amino Nitrogen ◽  
Essential Amino Acids ◽  
Major Allergen ◽  
Structural Features ◽  
Covalent Bonds ◽  
Pea Protein

The aim of the work was to optimize the process of obtaining multicomponent protein compositions with high biological value and higher functional properties than the original vegetable protein products. Was realized studies to obtain biocomposites on the base of pea protein-oat protein and pea protein-rice protein. Developed composites were enriched with all limited amino acids. For each of the essential amino acids, the amino acid score was 100% and higher. Protein products used in these compositions are not in major allergen list, which allows to use these compositions in allergen-free products and specialized nutrition. To determine biosynthesis parameters for compositions from pea protein and various protein concentrates with the use of transglutaminase enzyme, was studied effect of concentration and exposition time on the amount of amino nitrogen released during the reaction. Decreasing of amino nitrogen in the medium indicated the occurrence of a protein synthesis reaction with the formation of new covalent bonds. Were determined optimal parameters of reaction: the hydromodule, the exposure time, the concentration of EP of the preparation, were obtained mathematical models. Studies on the functional properties of composites, the physicochemical properties of the proteins that make up their composition, and structural features will make it possible to determine the uses in the manufacture of food products based on their ability to bind fat, water, form foam, gels, and etc.

scholarly journals Burn-related Collagen Conformational Changes in ex vivo Porcine Skin using Raman Spectroscopy

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hanglin Ye ◽  
Rahul ◽  
Uwe Kruger ◽  
Tianmeng Wang ◽  
Sufei Shi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Raman Spectroscopy ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Structural Changes ◽  
Mechanical Response ◽  
Ex Vivo ◽  
Burn Severity ◽  
Porcine Skin ◽  
Disordered Structures

AbstractThis study utilizes Raman spectroscopy to analyze the burn-induced collagen conformational changes in ex vivo porcine skin tissue. Raman spectra of wavenumbers 500–2000 cm−1 were measured for unburnt skin as well as four different burn conditions: (i) 200 °F for 10 s, (ii) 200 °F for the 30 s, (iii) 450 °F for 10 s and (iv) 450 °F for 30 s. The overall spectra reveal that protein and amino acids-related bands have manifested structural changes including the destruction of protein-related functional groups, and transformation from α-helical to disordered structures which are correlated with increasing burn severity. The deconvolution of the amide I region (1580–1720 cm−1) and the analysis of the sub-bands reveal a change of the secondary structure of the collagen from the α-like helix dominated to the β-aggregate dominated one. Such conformational changes may explain the softening of mechanical response in burnt tissues reported in the literature.

Essential amino acids and their need by lactating cows

2020 ◽  
pp. 30-46
Author(s):  
V. Ryadchikov ◽  
A. Tantawi
Keyword(s):  
Amino Acids ◽  
Crude Protein ◽  
Milk Protein ◽  
Protein Biosynthesis ◽  
Essential Amino Acids ◽  
Absolute Number ◽  
Factorial Method ◽  
Lactating Cows ◽  
Metabolic Protein ◽  
Daily Milk Yield

Metabolic protein is the main source of truly absorbed amino acids. The determination of metabolic protein and metabolic acids is an important, but very difficult task. To do this, you need to know the exact number of incoming protein fractions in the small intestine as part of the duodenal fl ow of chymus, their digestibility, the fl ow of metabolism of essential amino acids from the intestine to the bloodstream and the coefficients of their use for milk protein biosynthesis and maintenance of life. The purpose of the research was to determine the need of lactating cows for metabolic essential amino acids by factorial method. During the researches, developed standards needs to metabolic essential amino acids for lactating cows (g/kg) milk with a content of 3,3 % (33 g/kg) crude protein and 3,15 % (31,5 g/kg) of pure protein and to maintain 1 kg/body weight 0,75, which allows to calculate the daily requirement in the absolute number of amino acids (g). The assessment of security of rations of lactating cows metabolic lysine and methionine has been shown coincidence with the norms of needs in the amount of 93 %; daily milk yield of natural milk under this provision of lysine and methionine were 38,7 % and 39,4. The availability of metabolic methionine was at the level of 77-85 %, which is explained by the unprocessed coefficients of transformation of metabolic methionine into pure methionine of milk protein. In the total duodenal fl ow of amino acids approximately 60-70 % is microbial protein and 30-40 % is non-degradable protein in the rumen. It has been found that the digestibility of dry and organic matter in the rumen and the general digestive tract in relation to UDP:DP 35: 65 % crude protein is 2-3 % (absolute) higher than for UDP:DP = 50:50 % crude protein.

Protein Quality, Secondary Structure and Effect of Physicochemical Factors on Emulsifying Properties of Irvingia gabonensis Almonds

2019 ◽  
Vol 15 (4) ◽  
pp. 367-375
Author(s):  
Martin A. Mune Mune ◽  
Christian B. Bassogog ◽  
Pierre A. Bayiga ◽  
Carine E. Nyobe ◽  
Samuel R. Minka
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Secondary Structure ◽  
Protein Quality ◽  
Low Cost ◽  
Protein Solubility ◽  
Essential Amino Acids ◽  
Emulsifying Properties ◽  
Food Ingredient ◽  
Irvingia Gabonensis

Background: There is a constant search of new plant proteins, with adequate nutritional and functional properties, as well as bioactive properties and low-cost for utilization in various food formulations. Objective: The aim of this work was to access the nutritional and functional potential of protein from Irvingia gabonensis, for utilization as ingredient or supplement in food. Methods: Proximate composition and amino acid were analyzed. Nutritional parameters were calculated from amino acid composition. Physicochemical properties and secondary structure of protein were determined. Finally, effect of oil to water ratio (OWR), pH and concentration on emulsifying properties was analyzed. Results: The flour contained 22.26% protein, 5.30% ash and 60% carbohydrates. Proteins contained all essential amino acids, with high content of Leu, Ile, Val, Thr and sulfur-containing amino acids. Essential amino acid index (69%), protein efficiency ratio (2.39-2.63) and biological value (79.91%) were studied. The maximum protein solubility (61%) was noticed at pH 8, while high hydrophobicity was observed at pH 2. A transition from an irregular secondary structure to a more ordered structure was found from pH 2-4 to pH 6-10. pH, OWR and concentration significantly affected emulsifying properties of Irvingia gabonensis almonds. The maximum emulsifying capacity (EC) was observed under acidic pH and high flour concentration. EC increased with increasing OWR and concentration, while decreased with increasing pH. High ES (25-35%) was observed at pH 4-8 and OWR of 1/3 to 1/2 (v/v), at flour concentration of 3-4% (w/v). Conclusion: Irvingia gabonensis showed good potential as food ingredient or supplement.

scholarly journals SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3260 ◽  
Author(s):  
Abdollah Dehzangi ◽  
Yosvany López ◽  
Ghazaleh Taherzadeh ◽  
Alok Sharma ◽  
Tatsuhiko Tsunoda
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
High Sensitivity ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Sumoylation Site ◽  
Translation Process ◽  
Wide Range

Post Translational Modification (PTM) is defined as the modification of amino acids along the protein sequences after the translation process. These modifications significantly impact on the functioning of proteins. Therefore, having a comprehensive understanding of the underlying mechanism of PTMs turns out to be critical in studying the biological roles of proteins. Among a wide range of PTMs, sumoylation is one of the most important modifications due to its known cellular functions which include transcriptional regulation, protein stability, and protein subcellular localization. Despite its importance, determining sumoylation sites via experimental methods is time-consuming and costly. This has led to a great demand for the development of fast computational methods able to accurately determine sumoylation sites in proteins. In this study, we present a new machine learning-based method for predicting sumoylation sites called SumSec. To do this, we employed the predicted secondary structure of amino acids to extract two types of structural features from neighboring amino acids along the protein sequence which has never been used for this task. As a result, our proposed method is able to enhance the sumoylation site prediction task, outperforming previously proposed methods in the literature. SumSec demonstrated high sensitivity (0.91), accuracy (0.94) and MCC (0.88). The prediction accuracy achieved in this study is 21% better than those reported in previous studies. The script and extracted features are publicly available at: https://github.com/YosvanyLopez/SumSec.

scholarly journals Expression of rat alpha 1 Na,K-ATPase containing substitutions of “essential” amino acids in the catalytic center.

1993 ◽  
Vol 268 (24) ◽  
pp. 17930-17934
Author(s):  
L.K. Lane ◽  
J.M. Feldmann ◽  
C.E. Flarsheim ◽  
C.L. Rybczynski
Keyword(s):  
Amino Acids ◽  
Essential Amino Acids ◽  
Catalytic Center

scholarly journals Structure of a fungal form of aspartate semialdehyde dehydrogenase fromCryptococcus neoformans

2015 ◽  
Vol 71 (11) ◽  
pp. 1365-1371 ◽  
Author(s):  
Gopal Dahal ◽  
Ronald E. Viola
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Drug Design ◽  
Cryptococcus Neoformans ◽  
Biosynthetic Pathway ◽  
Essential Amino Acids ◽  
Structural Features ◽  
Antimicrobial Drug ◽  
Semialdehyde Dehydrogenase

Aspartate semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate-biosynthetic pathway and represents a valid target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. Production of this intermediate represents the first committed step in the biosynthesis of the essential amino acids methionine, isoleucine and threonine in fungi, and also the amino acid lysine in bacteria. The structure of a new fungal form of ASADH fromCryptococcus neoformanshas been determined to 2.6 Å resolution. The overall structure ofCnASADH is similar to those of its bacterial orthologs, but with some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs.

scholarly journals Intracellular Protein Biosynthesis: A Review

2020 ◽  
pp. 10-18
Author(s):  
Abdulsalam Alhalmi ◽  
Nafaa Alzobaidi ◽  
Amer Abdulrahman
Keyword(s):  
Amino Acids ◽  
Conformational Changes ◽  
Biological Function ◽  
Protein Biosynthesis ◽  
Genetic Material ◽  
Protein Molecule ◽  
Peptide Bond ◽  
Vital Role ◽  
Intracellular Protein ◽  
Specific Order

Proteins are macromolecules made up of many amino acids that linked together by peptide bond to make a protein molecule. The sequence and the number of amino acids determines each protein unique structure and specific function. Proteins play a vital role in living systems and play important biological functions. Biosynthesis of protein occur in our body cells in order to support the biological function in our body. Intracellular protein synthesis is a complex process that involve the transformation of information and instructions from a genetic material DNA inside the nucleus to form mRNA molecules that transferred to the cytoplasm and liked to the cytoplasmic ribosome. Subsequently, the m RNA and further encode a sequence of amino acid in a specific order and number to form a polypeptide chains that finally undergoes conformational changes and folding to form a particular structure protein. This review will focus on the tow consecutive stages of protein biosynthesis; transcription and translation, and their substage processes; initiation, elongation, and termination. Briefly, overview the role of protein in the biological function and the different types of protein structure.

scholarly journals Sequence conservation and structural features that are common within TRP channels

2021 ◽  
Author(s):  
Deny Cabezas-Bratesco ◽  
Charlotte K. Colenso ◽  
Katina Zavala ◽  
Danielle Granata ◽  
Vincenzo Carnevale ◽  
...  
Keyword(s):  
Amino Acids ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Trp Channels ◽  
Three Dimensional ◽  
Large Family ◽  
Structural Features ◽  
Large Set ◽  
Voltage Gated ◽  
The Core

TRP proteins are a large family of cation selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state of the channel are still missing for TRP channels. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed bioinformatic analyses over a large set of TRP channel genes. Here we report a discrete and exceptionally conserved set of residues. This fingerprint is composed of eleven residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbors the apparent differences in coupling strategies used by TRP subgroups.

Pengoptimalan Air Leri dalam Pembuatan Sabun Pembersih Wajah Alami yang Ekonomis

2017 ◽  
Vol 3 (1) ◽  
Author(s):  
Rahmawati Rahmawati ◽  
Trimayasari Trimayasari ◽  
Ghozali Akhmad Mustaqim ◽  
Wening Dwi Prastiwi ◽  
Emas Agus Prastyo Wibowo
Keyword(s):  
Amino Acids ◽  
Fine Particles ◽  
Hard Water ◽  
Essential Amino Acids ◽  
Ultraviolet Rays ◽  
Starch Granules ◽  
Facial Skin ◽  
Skin Cells ◽  
The Face ◽  
Made In

AbstractSoap facial cleanser is needed to keep the facial skin to keep them clean and healthy. The purpose of this study to make soap cleanser with natural materials such as hard water deposits leri. This is because the use of leri water starch or starch granules of fine particles contained in water leri dansel dust can shed the dead skin on the face because of the essential amino acids contained can regenerate skin cells. In addition, water leri can brighten the face because the leri water oryzanol contain substances that can update the development and formation of the pigment melanin, which is effectively to ward off ultraviolet rays. The process of making soap using the principle of saponification reaction, namely the reaction between the oil and the KOH/NaOH. Facial cleansing soap made in this study is solid soap. Based on the results of quality test, soap solid leri water has a pH of 11.1, saponification number is 33, the water content of 46% as well as respondents to the test aspects of aroma and foam shows good results so this water leri treatment can be an alternative solution to prevent the use of soap facial cleansers that contain harmful chemicals. Keywords: air leri, soap cleanser, saponification  AbstrakSabun pembersih wajah sangat diperlukan untuk menjaga kulit wajah agar tetap bersih dan sehat. Tujuan dari penelitian ini untuk membuat sabun pembersih wajah dengan bahan alami berupa endapan air leri. Penggunaan air leri ini dikarenakan butiran partikel starch atau pati halus yang terdapat dalam air leri dapat merontokkan debu dansel kulit mati pada wajah karena asam amino esensial yang terkandung dapat meregenerasi sel-sel kulit. Selain itu, air leri dapat mencerahkan wajah karena air leri mengandung zat oryzanol yang dapat memperbarui perkembangan dan pembentukan pigmen melanin, yang efektif guna menangkal sinar ultraviolet. Proses pembuatan sabun menggunakan prinsip reaksi saponifikasi, yaitu reaksi antara minyak dan KOH/NaOH. Sabun pembersih wajah yang dibuat dalam penelitian ini ialah sabun padat. Berdasarkan hasil uji mutu, sabun air leri padat memiliki pH 11,1, angka penyabunan sebesar 33 kadar air 46 kadar air 46 % serta uji responden terhadap aspek aroma dan busa yang menunjukkan hasil cukup baik sehingga pengolahan air leri ini dapat menjadi solusi alternative untuk mencegah penggunaan sabun pembersih wajah yang mengandung bahan kimia berbahaya. Kata kunci: air leri, sabun pembersih wajah, saponifikasi 

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