scholarly journals Comparative functional analysis of proteins containing low-complexity predicted amyloid regions

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5823 ◽  
Author(s):  
Bandana Kumari ◽  
Ravindra Kumar ◽  
Vipin Chauhan ◽  
Manish Kumar
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aromatic Amino Acids ◽  
Low Complexity ◽  
Amyloid Formation ◽  
Charged Amino Acids ◽  
Human Proteins ◽  
Hydrophobic Amino Acids ◽  
Compositional Pattern ◽  
Positively Charged

Background In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their uncontrolled expansion and amyloid formation. But a comparative analysis of the behavior of LCR based on their constituent amino acids and their association with amyloidogenic propensity is not available. Methods Firstly we grouped all LCRs on the basis of their composition: homo-polymers, positively charged amino acids, negatively charged amino acids, polar amino acids and hydrophobic amino acids. We analyzed the compositional pattern of LCRs in each group and their propensity to form amyloids. The functional characteristics of proteins containing different groups of LCRs were explored using DAVID. In addition, we also analyzed the classes, pathways and functions of human proteins that form amyloids in LCRs. Results Among homopolymeric LCRs, the most common was Gln repeats. LCRs composed of repeats of Met and aromatic amino acids were amongst the least occurring. The results revealed that LCRs composed of negatively charged and polar amino acids were more common in comparison to LCRs formed by positively charged and hydrophobic amino acids. We also noted that generally proteins with LCRs were involved in transcription but those with Gly repeats were associated to translational activities. Our analysis suggests that proteins in which LCR is composed of hydrophobic residues are more prone toward amyloid formation. We also found that the human proteins with amyloid forming LCRs were generally involved in binding and catalytic activity. Discussion The presented analysis summarizes the most common and least occurring LCRs in proteins. Our results show that though repeats of Gln are the most abundant but Asn repeats make longest stretch of low complexity. The results showed that potential of LCRs to form amyloids varies with their amino acid composition.

Amino Acid Dependent Performance of Modified Chitosan Against Bacteria and Red Blood Cell

2021 ◽  
Vol 21 (11) ◽  
pp. 5443-5448
Author(s):  
Xiaoyan Ju ◽  
Lu Tian ◽  
Xuantong Duan ◽  
Zhuang Li ◽  
Yongping Han ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Antibacterial Agents ◽  
Molecular Design ◽  
Antibacterial Properties ◽  
E Coli ◽  
Modified Chitosan ◽  
Charged Amino Acids ◽  
Hydrophobic Amino Acids ◽  
Positively Charged

In order to combat antibiotic resistance, the development of new antibacterial agents is essential. In this study, we prepared four types of amino acid modified chitosan (CS-AA). Compared with chitosan modified with hydrophobic amino acids, the chitosan modified with positively charged amino acids showed higher antibacterial efficiency against Escherichia coli (E. coli) under similar grafting rate. CS-AA achieves antibacterial properties mainly by destroying the integrity of bacterial cell membranes. All the four types of CS-AA show low toxicity towards red blood cells. This work indicates that positively charged groups are more important than hydrophobic groups in the design of chitosan-based antibacterial agents, and provides helpful information for the molecular design of effective antibacterial agents.

Tetraphenyl porphyrin films as selective detectors for amino acid molecules

2020 ◽  
Vol 24 (10) ◽  
pp. 1215-1223
Author(s):  
Jesús Miguel Rivera ◽  
Margarita Rivera
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Quartz Crystal Microbalance ◽  
Quartz Crystal ◽  
Binding Energies ◽  
Charged Amino Acids ◽  
Tetraphenyl Porphyrin ◽  
Pseudo Second Order ◽  
Selective Detectors ◽  
Positively Charged

The interaction of different amino acids and vacuum evaporated tetraphenyl porphyrin films was investigated by using kinetic isotherms, UV-vis spectroscopy, quartz crystal microbalance and density functional theory techniques. The adsorption process was analyzed by using pseudo-first-order and pseudo-second-order models. From these results, the adsorption order changed depending on the chemical characteristics of the porphyrin film, although most of the interactions were classified as pseudo-second-order at the films interface. From absorbance measurements, red shifts on the Soret peak positions were observed for all amino acids interacting with the metal free and the ZnTPP systems, while the position of the Soret peak barely change for the CuTPP surface, except for a slight bathocromic shift for arginine. On the other hand, the broadening of the Soret peak was more important for the ZnTPP and H2TPP surfaces, but the interaction with the CuTPP interfaces decreased the width of the peaks in all cases. In addition, a quartz crystal microbalance analysis was employed to investigate the film sensing performance during amino acid exposure. From these results, positively charged amino acids were more easily adsorbed on the films in contrast with the polar (serine) molecule. DFT calculations exhibited important deformations for H2TPP, the out-of-plane displacement of the Zn atom for ZnTPP, and hydrogen bond interactions with the CuTPP molecule. DFT also showed high binding energies for the positively charged amino acids but low binding energies for serine in agreement with experimental data. From these results, porphyrin films could be used as selective detectors for various L-amino acid molecules.

scholarly journals Structure-Activity Relationship of Synthetic Variants of the Milk-Derived Antimicrobial Peptide αs2-Casein f(183–207)

2013 ◽  
Vol 79 (17) ◽  
pp. 5179-5185 ◽  
Author(s):  
Avelino Alvarez-Ordóñez ◽  
Máire Begley ◽  
Tanya Clifford ◽  
Thérèse Deasy ◽  
Kiera Considine ◽  
...  
Keyword(s):  
Amino Acids ◽  
Biological Activity ◽  
Amino Acid ◽  
Antimicrobial Peptide ◽  
Peptide Sequence ◽  
Content Type ◽  
Charged Amino Acids ◽  
Food Borne ◽  
Relationship Of ◽  
Positively Charged

ABSTRACTTemplate-based studies on antimicrobial peptide (AMP) derivatives obtained through manipulation of the amino acid sequence are helpful to identify properties or residues that are important for biological activity. The present study sheds light on the importance of specific amino acids of the milk-derived αs2-casein f(183–207) peptide to its antibacterial activity against the food-borne pathogensListeria monocytogenesandCronobacter sakazakii. Trimming of the peptide revealed that residues at the C-terminal end of the peptide are important for activity. Removal of the last 5 amino acids at the C-terminal end and replacement of the Arg at position 23 of the peptide sequence by an Ala residue significantly decreased activity. These findings suggest that Arg23 is very important for optimal activity of the peptide. Substitution of the also positively charged Lys residues at positions 15 and 17 of the αs2-casein f(183–207) peptide also caused a significant reduction of the effectiveness againstC. sakazakii, which points toward the importance of the positive charge of the peptide for its biological activity. Indeed, simultaneous replacement of various positively charged amino acids was linked to a loss of bactericidal activity. On the other hand, replacement of Pro residues at positions 14 and 20 resulted in a significantly increased antibacterial potency, and hydrophobic end tagging of αs2-casein f(193–203) and αs2-casein f(197–207) peptides with multiple Trp or Phe residues significantly increased their potency againstL. monocytogenes. Finally, the effect of pH (4.5 to 7.4), temperature (4°C to 37°C), and addition of sodium and calcium salts (1% to 3%) on the activity of the 15-amino-acid αs2-casein f(193–207) peptide was also determined, and its biological activity was shown to be completely abolished in high-saline environments.

scholarly journals Amino Acid Contacts between Sigma 70 Domain 4 and the Transcription Activators RhaS and RhaR

2004 ◽  
Vol 186 (18) ◽  
pp. 6277-6285 ◽  
Author(s):  
Jason R. Wickstrum ◽  
Susan M. Egan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Level ◽  
Transcription Activation ◽  
Charged Amino Acids ◽  
Specific Contact ◽  
Loss Of Contact ◽  
Transcription Activators ◽  
Sigma 70 ◽  
Positively Charged

ABSTRACT The RhaS and RhaR proteins are transcription activators that respond to the availability of l-rhamnose and activate transcription of the operons in the Escherichia coli l-rhamnose catabolic regulon. RhaR activates transcription of rhaSR, and RhaS activates transcription of the operon that encodes the l-rhamnose catabolic enzymes, rhaBAD, as well as the operon that encodes the l-rhamnose transport protein, rhaT. RhaS is 30% identical to RhaR at the amino acid level, and both are members of the AraC/XylS family of transcription activators. The RhaS and RhaR binding sites overlap the −35 hexamers of the promoters they regulate, suggesting they may contact the σ70 subunit of RNA polymerase as part of their mechanisms of transcription activation. In support of this hypothesis, our lab previously identified an interaction between RhaS residue D241 and σ70 residue R599. In the present study, we first identified two positively charged amino acids in σ70, K593 and R599, and three negatively charged amino acids in RhaR, D276, E284, and D285, that were important for RhaR-mediated transcription activation of the rhaSR operon. Using a genetic loss-of-contact approach we have obtained evidence for a specific contact between RhaR D276 and σ70 R599. Finally, previous results from our lab separately showed that RhaS D250A and σ70 K593A were defective at the rhaBAD promoter. Our genetic loss-of-contact analysis of these residues indicates that they identify a second site of contact between RhaS and σ70.

scholarly journals Water follows polar and nonpolar protein surface domains

2019 ◽  
Vol 116 (39) ◽  
pp. 19274-19281 ◽  
Author(s):  
Baofu Qiao ◽  
Felipe Jiménez-Ángeles ◽  
Trung Dac Nguyen ◽  
Monica Olvera de la Cruz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Interactions ◽  
Protein Solubility ◽  
Protein Surface ◽  
Protein Surfaces ◽  
Charged Amino Acids ◽  
Average Water ◽  
Surface Domains ◽  
Positively Charged

The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.

scholarly journals Probing the Structural Determinants of Amino Acid Recognition: X-Ray Studies of Crystalline Ditopic Host-Guest Complexes of the Positively Charged Amino Acids, Arg, Lys, and His with a Cavitand Molecule

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3368 ◽  
Author(s):  
Giovanna Brancatelli ◽  
Enrico Dalcanale ◽  
Roberta Pinalli ◽  
Silvano Geremia
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Water Molecule ◽  
Rational Design ◽  
Structural Information ◽  
Amino Acid Side Chain ◽  
Structural Determinants ◽  
X Ray ◽  
Charged Amino Acids ◽  
Positively Charged

Crystallization of tetraphosphonate cavitand Tiiii[H, CH3, CH3] in the presence of positively charged amino acids, namely arginine, lysine, or histidine, afforded host-guest complex structures. The X-ray structure determination revealed that in all three structures, the fully protonated form of the amino acid is ditopically complexed by two tetraphosphonate cavitand molecules. Guanidinium, ammonium, and imidazolium cationic groups of the amino acid side chain are hosted in the cavity of a phosphonate receptor, and are held in place by specific hydrogen bonding interactions with the P=O groups of the cavitand molecule. In all three structures, the positively charged α-ammonium groups form H-bonds with the P=O groups, and with a water molecule hosted in the cavity of a second tetraphosphonate molecule. Furthermore, water-assisted dimerization was observed for the cavitand/histidine ditopic complex. In this 4:2 supramolecular complex, a bridged water molecule is held by two carboxylic acid groups of the dimerized amino acid. The structural information obtained on the geometrical constrains necessary for the possible encapsulation of the amino acids are important for the rational design of devices for analytical and medical applications.

scholarly journals Enhanced catalytic efficiency and universality of L-amino acid deaminase achieved by a shorter proton transfer distance

2021 ◽  
Author(s):  
Yaoyun Wu ◽  
Sheng Zhang ◽  
Wei Song ◽  
Jia Liu ◽  
Xiulai Chen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Catalytic Mechanism ◽  
Aromatic Amino Acids ◽  
Catalytic Efficiency ◽  
Charged Amino Acids ◽  
Keto Acids ◽  
Key Factor ◽  
Limiting Efficiency ◽  
Sulfur Containing

L-amino acid deaminase (LAAD, EC 1.4.3.2) catalyzes the deamination of α-amino acids. At present, sustainable enzymatic α-keto acids synthesis remains limited by the low catalytic efficiency of wild-type LAADs. In this study, catalytic mechanism was elucidated, and catalytic distance D1 between the substrate αC-H and the cofactor FAD N(5) was identified as the key factor limiting efficiency of Proteus mirabilis PmiLAAD. Shortening the distance via protein engineering improved catalytic efficiency toward six selected amino acids. The two variants with the best catalytic properties were W1, which exhibited a preference for short-chain aliphatic amino acids and charged amino acids, and W2, which showed a preference for large aromatic amino acids and sulfur-containing amino acids. The mutated residues in the two variants altered the binding pose of the substrate, α-hydrogen was improved to be more perpendicular against the plain of the isoalloxazine ring causing the angle between the substrates’ αC-H, FAD N(5), and FAD N(10) to approach 90°, and thus shortened the distance. Finally, W1 and W2 were cascade in one Escherichia coli cell to obtain strain S3, which exhibited conversion >90% and yield >100 g/L toward all selected substrates. These results provide the basis for improving industrial production of α-keto acids via microbial deamination of α-amino acids.

Single Amino Acid Based Self-Assemblies of Cysteine and Methionine

2018 ◽  
Author(s):  
Nidhi Gour ◽  
Bharti Koshti ◽  
Chandra Kanth P. ◽  
Dhruvi Shah ◽  
Vivek Shinh Kshatriya ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acids ◽  
Neutral Condition ◽  
Single Amino Acid ◽  
Binding Assays ◽  
Human Neuroblastoma ◽  
Cytotoxicity Assays ◽  
First Time

We report for the very first time self-assembly of Cysteine and Methionine to discrenible strucutres under neutral condition. To get insights into the structure formation, thioflavin T and Congo red binding assays were done which revealed that aggregates may not have amyloid like characteristics. The nature of interactions which lead to such self-assemblies was purported by coincubating assemblies in urea and mercaptoethanol. Further interaction of aggregates with short amyloidogenic dipeptide diphenylalanine (FF) was assessed. While cysteine aggregates completely disrupted FF fibres, methionine albeit triggered fibrillation. The cytotoxicity assays of cysteine and methionine structures were performed on Human Neuroblastoma IMR-32 cells which suggested that aggregates are not cytotoxic in nature and thus, may not have amyloid like etiology. The results presented in the manuscript are striking, since to the best of our knowledge,this is the first report which demonstrates that even non-aromatic amino acids (cysteine and methionine) can undergo spontaneous self-assembly to form ordered aggregates.

scholarly journals Avoided motifs: short amino acid strings missing from protein datasets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Function ◽  
Large Protein ◽  
New Approach ◽  
Cellular Context ◽  
Human Proteins ◽  
Context Specific ◽  
Protein Datasets

Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins specifically located in the cytoplasm, and two more in secreted proteins. Our results support the hypothesis that the characterization of Avoided Motifs in particular contexts can provide us with information about functional motifs, pointing to a new approach in the use of molecular sequences for the discovery of protein function.

scholarly journals The Superagonistic Activity of Bovine Thyroid-stimulating Hormone (TSH) and the Human TR1401 TSH Analog Is Determined by Specific Amino Acids in the Hinge Region of the Human TSH Receptor

2009 ◽  
Vol 284 (24) ◽  
pp. 16317-16324 ◽  
Author(s):  
Sandra Mueller ◽  
Gunnar Kleinau ◽  
Mariusz W. Szkudlinski ◽  
Holger Jaeschke ◽  
Gerd Krause ◽  
...  
Keyword(s):  
Amino Acids ◽  
Thyroid Stimulating Hormone ◽  
Hinge Region ◽  
Camp Production ◽  
Glycoprotein Hormone ◽  
Charged Amino Acids ◽  
Bovine Thyroid ◽  
Positively Charged ◽  
Bovine Tsh ◽  
Signaling Activity

Bovine TSH (bTSH) has a higher affinity to the human TSHR (hTSHR) and a higher signaling activity than human TSH (hTSH). The molecular reasons for these phenomena are unknown. Distinct negatively charged residues (Glu297, Glu303, and Asp382) in the hinge region of the hTSHR are known to be important for bTSH binding and signaling. To investigate the potential relevance of these positions for differences between bTSH and hTSH in the interaction to the hTSHR, we determined bTSH- and hTSH-mediated cAMP production of several substitutions at these three hinge residues. To examine specific variations of hTSH, we also investigated the superagonistic hTSH analog TR1401 (TR1401), whose sequence differs from hTSH by four additional positively charged amino acids that are also present in bTSH. To characterize possible interactions between the acidic hTSHR positions Glu297, Glu303, or Asp382 and the additional basic residues of TR1401, we investigated TR1401 binding and signaling properties. Our data reveal increased cAMP signaling of the hTSHR using TR1401 and bTSH compared with hTSH. Whereas Asp382 seems to be important for bTSH- and TR1401-mediated but not for hTSH-mediated signaling, the substitution E297K exhibits a decreased signaling for all three TSH variants. Interestingly, bTSH and TR1401 showed only a slightly different binding pattern. These observations imply that specific residues of the hinge region are mediators of the superagonistic activity of bTSH and TR1401 in contrast to hTSH. Moreover, the simultaneous localization of binding components in the glycoprotein hormone molecule and the receptor hinge region permits important reevaluation of interacting hormone receptor domains.

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