Distribution Pattern Of Amino Acids Research Articles

Dissecting peripheral protein-membrane interfaces.

Peripheral membrane proteins (PMPs) include a wide variety of proteins that have in common to bind transiently to the chemically complex interfacial region of membranes through their interfacial binding site (IBS). In contrast to protein-protein or protein-DNA/RNA interfaces, peripheral protein-membrane interfaces are poorly characterized. We collected a dataset of PMP domains representative of the variety of PMP functions: membrane-targeting domains (Annexin, C1, C2, discoidin C2, PH, PX), enzymes (PLA, PLC/D) and lipid-transfer proteins (START). The dataset contains 1328 experimental structures and 1194 AphaFold models. We mapped the amino acid composition and structural patterns of the IBS of each protein in this dataset, and evaluated which were more likely to be found at the IBS compared to the rest of the domains' accessible surface. In agreement with earlier work we find that about two thirds of the PMPs in the dataset have protruding hydrophobes (Leu, Ile, Phe, Tyr, Trp and Met) at their IBS. The three aromatic amino acids Trp, Tyr and Phe are a hallmark of PMPs IBS regardless of whether they protrude on loops or not. This is also the case for lysines but not arginines suggesting that, unlike for Arg-rich membrane-active peptides, the less membrane-disruptive lysine is preferred in PMPs. Another striking observation was the over-representation of glycines at the IBS of PMPs compared to the rest of their surface, possibly procuring IBS loops a much-needed flexibility to insert in-between membrane lipids. The analysis of the 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms. Besides revealing novel amino acids patterns at protein-membrane interfaces, our work contributes a new PMP dataset and an analysis pipeline that can be further built upon for future studies of PMPs properties, or for developing PMPs prediction tools using for example, machine learning approaches.

Protein Content and Amino Acid Profiles of Selected Edible Insect Species from the Democratic Republic of Congo Relevant for Transboundary Trade across Africa.

This study analyzed the protein content of ten edible insect species (using the Dumas method), then focused on the amino acid (AA) profiles of the six major commercially relevant species using HPLC (high-pressure (or performance) liquid chromatography). The protein contents varied significantly from 46.1% to 52.9% (dry matter); the Orthoptera representative yielding both the highest protein content and the highest values in three essential amino acids (EAAs). Regarding Lepidoptera species, the protein content of Saturniidae varied more than for Notodontidae. Imbrasia ertli gave the best example of a species that could be suggested for dietary supplementation of cereal-based diets, as the sample contained the highest values in five EAAs and for the EAA index. Furthermore, first-limiting AAs in the selected insects have also been pointed out (based on a species-specific AA score), supporting that the real benefit from eating insects is correlated to a varied diet. Additionally, preliminary insights into AA distribution patterns according to taxa provided three clusters based on protein quality and should be completed further to help tailor prescriptions of dietary diets. Since the AA composition of the selected insects was close to the FAO/WHO EAA requirement pattern for preschool children and met the requirements of 40% EAAs with high ratio EAAs/NEAAs, the current study endorses reports of edible insects as nutrient-rich and sustainable protein sources.

Systematically Studying the Optimal Amino Acid Distribution Patterns of the Amphiphilic Structure by Using the Ultrashort Amphiphiles.

Amphipathicity has traditionally been considered to be essential for the de novo design or systematic optimization of antimicrobial peptides (AMPs). However, the current research methods to study the relationship between amphiphilicity and antimicrobial activity are inappropriate, because the key parameters (hydrophobicity, positive charge, etc.) and secondary structure of AMPs are changed. To systematically and accurately study the effects of amphiphilicity on antimicrobial properties of AMPs, we designed parallel series of AMPs with a different order of amino acids in a sequence composed only of Arg and either Trp (WR series) or Leu (LR series), under conditions in which other vital parameters were fixed. Furthermore, based on the WR and LR peptides that can form stable amphiphilic β-sheet structures in the anionic membrane-mimetic environment, we found that high β-sheet amphipathic was accompanied by strong antimicrobial activity. Of such peptides, W5 ([RW]4W) and L5 ([RL]4L) with a nicely amphipathic β-sheet structure possessed the optimal therapeutic index. W5 and L5 also exhibited high stability in vitro and a potent membrane-disruptive mechanism. These results suggest that the alternate arrangement of hydrophobic and hydrophilic residues to form a stable amphipathic β-sheet structure is an essential factor that significantly affects the antimicrobial properties.

Effects of Geochemical and Environmental Parameters on Abiotic Organic Chemistry Driven by Iron Hydroxide Minerals

AbstractGeological conditions play a significant role in prebiotic/abiotic organic chemistry, especially when reactive minerals are present. Previous studies of the prebiotic synthesis of amino acids and other products in mineral‐containing systems have shown that a diverse array of compounds can be produced, depending on the experimental conditions. However, these previous experiments have not simulated the effects of varying geochemical conditions, in which factors such as pH, iron redox state, or chemical concentrations may vary over time and space in a natural environment. In geochemical systems that contain overlapping gradients, many permutations of individual conditions could exist and affect the outcome of an organic reaction network. We investigated reactions of pyruvate and glyoxylate, two compounds that are central to the emergence of metabolism, in simulated geological gradients of redox, pH, and ammonia concentration. Our results show that the positioning of pyruvate/glyoxylate reactions in this environmental parameter space determines the organic product distribution that results. Therefore, the distribution pattern of amino acids and alpha‐hydroxy acids produced prebiotically in a system reflects the specific reaction conditions, and would be distinct at various locations in an environment depending on local geochemistry. This is significant for origin of life chemistry in which the composition and function of oligomers could be affected by the environmentally driven distribution of monomers available. Also, for astrobiology and planetary science where organic distribution patterns are sometimes considered as a possible biosignature, it is important to consider environmentally driven abiotic organic reactions that might produce similar effects.

Control of human VDAC-2 scaffold dynamics by interfacial tryptophans is position specific

Membrane proteins employ specific distribution patterns of amino acids in their tertiary structure for adaptation to their unique bilayer environment. The solvent-bilayer interface, in particular, displays the characteristic ‘aromatic belt’ that defines the transmembrane region of the protein, and satisfies the amphipathic interfacial environment. Tryptophan—the key residue of this aromatic belt—is known to influence the folding efficiency and stability of a large number of well-studied α-helical and β-barrel membrane proteins. Here, we have used functional and biophysical techniques coupled with simulations, to decipher the contribution of strategically placed four intrinsic tryptophans of the human outer mitochondrial membrane protein, voltage-dependent anion channel isoform-2 (VDAC-2). We show that tryptophans help in maintaining the structural and functional integrity of folded hVDAC-2 barrel in micellar environments. The voltage gating characteristics of hVDAC-2 are affected upon mutation of tryptophans at positions 75, 86 and 221. We observe that Trp-160 and Trp-221 play a crucial role in the folding pathway of the barrel, and once folded, Trp-221 helps stabilize the folded protein in concert with Trp-75 and Trp-160. We further demonstrate that substituting Trp-86 with phenylalanine leads to the formation of stable barrel. We find that the region comprising strand β4 (Trp-86) and β10-14 (Trp-160 and Trp-221) display slower and faster folding kinetics, respectively, providing insight into a possible directional folding of hVDAC-2 from the C-terminus to N-terminus. Our results show that residue selection in a protein during evolution is a balancing compromise between optimum stability, function, and regulating protein turnover inside the cell.

High specific selectivity and Membrane-Active Mechanism of the synthetic centrosymmetric α-helical peptides with Gly-Gly pairs.

We used a template-assisted approach to develop synthetic antimicrobial peptides, which differ from naturally occurring antimicrobial peptides that can compromise host natural defenses. Previous researches have demonstrated that symmetrical distribution patterns of amino acids contribute to the antimicrobial activity of natural peptides. However, there is little research describing such design ideas for synthetic α-helical peptides. Therefore, here, we established a centrosymmetric α-helical sequence template (y + hhh + y)n (h, hydrophobic amino acid; +, cationic amino acid; y, Gly or hydrophobic amino acid), which contributed to amphipathicity, and a series of centrosymmetric peptides was designed with pairs of small amino acids (Ala and Gly), which were utilized to modulate the biological activity. The centrosymmetric peptides with 3 repeat units exhibited strong antimicrobial activity; in particular, the Gly-rich centrosymmetric peptide GG3 showed stronger selectivity for gram-negative bacteria without hemolysis. Furthermore, beyond our expectation, fluorescence spectroscopy and electron microscopy analyses indicated that the GG3, which possessed poor α-helix conformation, dramatically exhibited marked membrane destruction via inducing bacterial membrane permeabilization, pore formation and disruption, even bound DNA to further exert antimicrobial activity. Collectively, the Gly-rich centrosymmetric peptide GG3 was an ideal candidate for commercialization as a clinical therapeutic to treat gram-negative bacterial infections.

Amino acids and hexosamines in the Hess Rise core during the past 220,000 years

Core sediment samples collected from the Hess Rise, North Pacific, were analyzed for 20 common amino acids (AA) and two hexosamines (HA) to understand the relation between glacial–interglacial variations and deposition/preservation of sedimentary organic matter (OM). The sediments are predominantly carbonaceous (carbonates 35–80%). AA-based parameters—aspartic acid/glycine ratio and serine+threonine relative mole content—suggest that calcareous plankton was the major source of OM in these sediments. This inference is supported by the similarity in distribution patterns of AA and HA contents with that of organic carbon. Low values of AA/HA and glucosamine/galactosamine ratios (average 4.4 and 1.1, respectively) imply that much of the planktonic OM was replaced by microbial OM. The relative molar concentration of two nonprotein AA (β-alanine and γ-aminobutyric acid) varied with age of sediments; i.e., they were less abundant in recent sediments and more abundant in the oldest sediments. This trend is an indicator of extremely slow but continuous enzymatic degradation of proteinaceous OM within the sediments. So far, bulk OM has been believed to be one of the best proxies for estimation of primary productivity. However, it may be an underestimate, even for the late Quaternary sediments. Comparison of AA and HA content variations with SPECMAP stack revealed their enhanced deposition and preservation during glacial periods relative to interglacial periods. This, in turn, affected not only the planktonic production in surface waters but also the benthic community, including bacteria on the seafloor.

Excretion of amino acids by humans during space flight

We measured the urine amino acid distribution patterns before, during and after space flight on the Space Shuttle. The urine samples were collected on two separate flights of the space shuttle. The first flight lasted 9.5 days and the second flight 15 days. Urine was collected continuously on 8 subjects for the period beginning 10 d before launch to 6 d after landing. Results: In contrast to the earlier Skylab missions where a pronounced amino aciduria was found, on shuttle the urinary amino acids showed little change with spaceflight except for a marked decrease in all of the amino acids on FD (flight day) 1 (p < 0.05) and a reduction in isoleucine and valine on FD3 and FD4 (p < 0.05). Conclusions: (i) Amino aciduria is not an inevitable consequence of space flight, (ii) The occurrence of amino aciduria, like muscle protein breakdown is a mission specific effect rather than part of the general human response to microgravity.

Amino acid distribution in some fungal melanins and of soil humic acids from Brazil

Humic acids from four Brazilian topsoils of different origins and four soil fungal melanins, synthesized under two cultural conditions, were subjected to 6N HCl hydrolysis and their amino acid distribution patterns qualitatively and quantitatively determined. Both soil and fungal polymers showed similar patterns with aspartic acid, glutamic acid, glycine and alanine as the dominant amino acids. Some variations noted were more quantitative than qualitative, the similarities were more pronounced than differences, indicating that the fungal melanins may play a significant role in the formation of soil humic acid polymers. The humic acids of Brazilian soils had amino acid distribution patterns similar to those reported for humic acids of other tropical and temperate soils.

Sulphur amino acids and free amino acids in cotyledons of germinated seedlings ofAlbizzia lebbeck Benth exposed to different light intensities

Metabolism of sulphur amino acids and free amino acids has been studied in the cotyledons during germination ofAlbizzia lebbeck Benth seeds under different light intensities. Seeds ofA. lebbeck contain a large amount of sulphur amino acids which are rapidly utilised during early stages of germination A similarity in the distribution pattern of amino acids in cotyledon samples raised from different seed stocks is noticed. The level of amino acids was higher in the illuminated samples as compared to dark controls. The higher concentration of asparagine, and SAAII during the seedling growth with the increase in light intensities compared to dark-grown seedlings as well as initial seed sample may indicate the involvement of light-triggered reactions in the synthesis of these metabolites.

Biochemistry and microbiology of some Irish Sea sediments: I. Amino-acid analyses

Cores of sedimentary mud, collected on a transect between the Isle of Man and Ireland, were qualitatively analysed for free amino acids by thin-layer chromatography of the dansylated (DNS) derivatives. The DNS derivatives of isoleucine/leucine and α-aminobutyric acid were found in all samples, while the derivatives of phenylalanine, valine, arginine and ammonia were usually present. Acid hydrolysis followed by treatment with ninhydrin showed the presence of peptidyl amino acids in half the DNS-reacted extracts. No distribution pattern of amino acids was found either with geographical location or down the depths of the cores. Attempts to quantify the method were unsuccessful. Other analyses indicated the presence of glucose/galactose, but no neutral or phospholipids or recognizable plant pigments were identified.

Amino Acid Distribution Patterns in Soils

It has been almost definitely established by soil scientists that 37-50 per cent of the nitrogen of the soil is of proteinaceous nature. Though considerable work has been done along these lines in other countries no work has been done so far on the nature of soil nitrogen in the soils of South India with special reference to amino acid distribution patterns. The object of the present investigation, reported in this section, is to detect the protein components i. e., amino acids of soil hydrolysates and identification of the amino acids present in the typical soil types of the Madras and Kerala States of South India.

Amino-acid activation by individual enzymes.

I should like to comment on one aspect of Dr Gutfreund’s interesting paper. As he mentioned, we have found evidence that amino acids, after becoming enzymically activated by ATP through the formation of an enzyme-bound amino acyladenylate compound, are transferred to a low molecular weight RNA which, by accident or design, resides in the same crude activating enzyme fraction. It is gratifying that Dr Gutfreund has found a distribution pattern of amino acids on this RNA which roughly agrees with the pattern in the major protein products of mammary tissue. He points out, however, that there is no such correlation when one looks at the pattern of amino-acid activation. Indeed, because of this anomaly, some workers have devised theories of activation involving transacylation steps to account for activation of those amino acids for which an enzyme has not been found. Dr Gutfreund implies that there is much confusion and mystery here, and even suggests that the specificity of activation might be accounted for by soluble RNA , rather than by individual enzymes.