scholarly journals Color-tuning of natural variants of heliorhodopsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Se-Hwan Kim ◽  
Kimleng Chuon ◽  
Shin-Gyu Cho ◽  
Ahreum Choi ◽  
Seanghun Meas ◽  
...  
Keyword(s):  
3D Structure ◽  
Site Directed Mutagenesis ◽  
Type I ◽  
Transmembrane Helices ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Spectral Changes ◽  
His Tag ◽  
Natural Variants ◽  
Retinal Chromophore

AbstractMicrobial rhodopsins are distributed through many microorganisms. Heliorhodopsins are newly discovered but have an unclear function. They have seven transmembrane helices similar to type-I and type-II rhodopsins, but they are different in that the N-terminal region of heliorhodopsin is cytoplasmic. We chose 13 representative heliorhodopsins from various microorganisms, expressed and purified with an N-terminal His tag, and measured the absorption spectra. The 13 natural variants had an absorption maximum (λmax) in the range 530–556 nm similar to proteorhodopsin (λmax = 490–525 nm). We selected several candidate residues that influence rhodopsin color-tuning based on sequence alignment and constructed mutants via site-directed mutagenesis to confirm the spectral changes. We found two important residues located near retinal chromophore that influence λmax. We also predict the 3D structure via homology-modeling of Thermoplasmatales heliorhodopsin. The results indicate that the color-tuning mechanism of type-I rhodopsin can be applied to understand the color-tuning of heliorhodopsin.

scholarly journals Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

2020 ◽  
Author(s):  
Chi-Yun Lin ◽  
Steven Boxer
Keyword(s):  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Stokes Shift ◽  
Site Directed Mutagenesis ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Donor Acceptor ◽  
Form Model ◽  
Gfp Chromophore ◽  
Green Fluorescent

The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferable for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found the color of the neutral chromophore to be much more sensitive to protein electrostatics. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model compared with that of the anionic state, which requires only two forms. Specifically, an underlying zwitterionic charge transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to the protonated chromophore’s photoacidity and excited-state proton transfer (ESPT), we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of two-form model for donor–acceptor systems with localized electronic distributions.

In Vitro Characterisation of Two Naturally Occurring Mutations in the Thrombin-sensitive Region of Anticoagulant Protein S

1999 ◽  
Vol 82 (12) ◽  
pp. 1627-1633 ◽  
Author(s):  
Tusar Giri ◽  
Pablo García de Frutos ◽  
Tomio Yamazaki ◽  
Bruno Villoutreix ◽  
Björn Dahlbäck
Keyword(s):  
Molecular Modelling ◽  
Mammalian Cells ◽  
Recombinant Protein Expression ◽  
3D Structure ◽  
Protein S ◽  
Site Directed Mutagenesis ◽  
Type I ◽  
Sensitive Region ◽  
Naturally Occurring

SummaryThe molecular consequences of two naturally occurring mutations in the thrombin-sensitive region of protein S were investigated using a combination of recombinant protein expression, functional analysis and molecular modelling. Both mutations (R49H and R70S) have been found in thrombosis patients diagnosed as having type I protein S deficiency. Molecular modelling analysis suggested the R49H substitution not to disrupt the structure of thrombin-sensitive region, whereas the R70S substitution could affect the 3D structure mildly. To elucidate the molecular consequences of these substitutions experimentally, site directed mutagenesis of protein S cDNA and expression in mammalian cells created the two mutants. The secretion profiles and functional anticoagulant activities of the protein S mutants were characterised. Secretion of the R49H mutant was similar to that of wild type protein S, whereas the R70S mutant showed moderately decreased expression. Neither of the mutants showed any major functional defects as cofactors to activated protein C (APC) in an APTT-based assay or in degradation of factor Va. However, both mutants demonstrated decreased activity in a factor VIIIa degradation assay, which in addition to APC and protein S also included factor V as synergistic APC cofactor. In conclusion, the R49H substitution did not produce a quantitative abnormality in vitro, raising doubts as to whether it caused the type I deficiency. In contrast, the experimental data obtained for the R70S mutant agrees well with the observed type I deficiency. Our study illustrates that in vitro experimental characterisation together with computer-based structural analysis are useful tools in the analysis of the relationship between naturally occurring mutations and clinical phenotypes.

scholarly journals Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

2020 ◽  
Author(s):  
Chi-Yun Lin ◽  
Steven Boxer
Keyword(s):  
Green Fluorescent Protein ◽  
Fluorescent Protein ◽  
Stokes Shift ◽  
Site Directed Mutagenesis ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Donor Acceptor ◽  
Form Model ◽  
Gfp Chromophore ◽  
Green Fluorescent

The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferable for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found the color of the neutral chromophore to be much more sensitive to protein electrostatics. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model compared with that of the anionic state, which requires only two forms. Specifically, an underlying zwitterionic charge transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to the protonated chromophore’s photoacidity and excited-state proton transfer (ESPT), we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of two-form model for donor–acceptor systems with localized electronic distributions.

scholarly journals Familial hemiplegic migraine type 2 due to a novel missense mutation in ATP1A2

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fabio Antonaci ◽  
Sabrina Ravaglia ◽  
Gaetano S. Grieco ◽  
Stella Gagliardi ◽  
Cristina Cereda ◽  
...  
Keyword(s):  
Case Reports ◽  
3D Structure ◽  
Familial Hemiplegic Migraine ◽  
Transmembrane Helices ◽  
Hemiplegic Migraine ◽  
Case Presentation ◽  
Italian Family ◽  
Protein Prediction ◽  
Functional Consequences

Abstract Background The mechanisms of genotype-phenotype interaction in Familiar Hemiplegic migraine type 2 (FHM2) are still far from clear. Different ATP1A2 mutations have been described, with a spectrum of phenotypes ranging from mild to severe. No genotype-phenotype correlations have been attempted. Case presentation We describe an Italian family with FHM and a missense ATP1A2 variant (L425H) not previously described. The clinical picture was mild in all the affected members. Conclusions Co-segregation of the variant with the aura phenotype was complete in this family, suggesting a 100% penetrance. In silico protein prediction softwares indicate that this variant may change the 3D structure of ATPA1A2 at the cytoplasmic loop between the two central transmembrane helices. Milder FHM phenotypes are rarely reported in literature, likely because case reports are biased towards the most severe phenotypes, with milder forms possibly misdiagnosed as sporadic migraine with aura forms (MAs), even with complex auras. Further studies taking into account intra-familiar variability and functional consequences on the channel protein may help clarify genotype-phenotype correlations.

scholarly journals Color Tuning Mechanism of Human Red, Green, and Blue Cone Pigments: SAC-CI Theoretical Study

2009 ◽  
Vol 82 (9) ◽  
pp. 1140-1148 ◽  
Author(s):  
Kazuhiro Fujimoto ◽  
Jun-ya Hasegawa ◽  
Hiroshi Nakatsuji
Keyword(s):  
Theoretical Study ◽  
Color Tuning ◽  
Tuning Mechanism ◽  
Cone Pigments

scholarly journals Recombinant Protein Truncation Strategy for Inducing Bactericidal Antibodies to the Macrophage Infectivity Potentiator Protein of Neisseria meningitidis and Circumventing Potential Cross-Reactivity with Human FK506-Binding Proteins

2014 ◽  
Vol 83 (2) ◽  
pp. 730-742 ◽  
Author(s):  
Magdalena K. Bielecka ◽  
Nathalie Devos ◽  
Mélanie Gilbert ◽  
Miao-Chiu Hung ◽  
Vincent Weynants ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Bactericidal Activity ◽  
Binding Proteins ◽  
Leader Peptide ◽  
Type I ◽  
Globular Domain ◽  
His Tag ◽  
Macrophage Infectivity Potentiator ◽  
Fk506 Binding Proteins ◽  
Macrophage Infectivity

A recombinant macrophage infectivity potentiator (rMIP) protein ofNeisseria meningitidisinduces significant serum bactericidal antibody production in mice and is a candidate meningococcal vaccine antigen. However, bioinformatics analysis of MIP showed some amino acid sequence similarity to human FK506-binding proteins (FKBPs) in residues 166 to 252 located in the globular domain of the protein. To circumvent the potential concern over generating antibodies that could recognize human proteins, we immunized mice with recombinant truncated type I rMIP proteins that lacked the globular domain and the signal leader peptide (LP) signal sequence (amino acids 1 to 22) and contained the His purification tag at either the N or C terminus (C-term). The immunogenicity of truncated rMIP proteins was compared to that of full (i.e., full-length) rMIP proteins (containing the globular domain) with either an N- or C-terminal His tag and with or without the LP sequence. By comparing the functional murine antibody responses to these various constructs, we determined that C-term His truncated rMIP (−LP) delivered in liposomes induced high levels of antibodies that bound to the surface of wild-type but not Δmipmutant meningococci and showed bactericidal activity against homologous type I MIP (median titers of 128 to 256) and heterologous type II and III (median titers of 256 to 512) strains, thereby providing at least 82% serogroup B strain coverage. In contrast, in constructs lacking the LP, placement of the His tag at the N terminus appeared to abrogate bactericidal activity. The strategy used in this study would obviate any potential concerns regarding the use of MIP antigens for inclusion in bacterial vaccines.

scholarly journals High-throughput functional analysis of natural variants in yeast

2021 ◽  
Author(s):  
Chiann-Ling C Yeh ◽  
Andreas Tsouris ◽  
Joseph Schacherer ◽  
Maitreya J. Dunham
Keyword(s):  
High Throughput ◽  
Site Directed Mutagenesis ◽  
Loss Of Function ◽  
Evolutionary Pattern ◽  
Intermediate Phenotypes ◽  
Sulfate Limitation ◽  
Long Read ◽  
Natural Variants ◽  
Natural Isolates ◽  
Error Correction Algorithm

How natural variation affects phenotype is difficult to determine given our incomplete ability to deduce the functional impact of the polymorphisms detected in a population. Although current computational and experimental tools can predict and measure allele function, there has previously been no assay that does so in a high-throughput manner while also representing haplotypes derived from wild populations. Here, we present such an assay that measures the fitness of hundreds of natural alleles of a given gene without site-directed mutagenesis or DNA synthesis. With a large collection of diverse Saccharomyces cerevisiae natural isolates, we piloted this technique using the gene SUL1, which encodes a high-affinity sulfate permease that, at increased copy number, can improve the fitness of cells grown in sulfate-limited media. We cloned and barcoded all alleles from a collection of over 1000 natural isolates en masse and matched barcodes with their respective variants using PacBio long-read sequencing and a novel error-correction algorithm. We then transformed the reference S288C strain with this library and used barcode sequencing to track growth ability in sulfate limitation of lineages carrying each allele. We show that this approach allows us to measure the fitness conferred by each allele and stratify functional and nonfunctional alleles. Additionally, we pinpoint which polymorphisms in both coding and noncoding regions are detrimental to fitness or are of small effect and result in intermediate phenotypes. Integrating these results with a phylogenetic tree, we observe how often loss-of-function occurs and whether or not there is an evolutionary pattern to our observable phenotypic results. This approach is easily applicable to other genes. Our results complement classic genotype-phenotype mapping strategies and demonstrate a high-throughput approach for understanding the effects of polymorphisms across an entire species which can greatly propel future investigations into quantitative traits.

scholarly journals Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15.

2014 ◽  
Vol 61 (4) ◽  
Author(s):  
Mohd Adilin Yaacob ◽  
Wan Atiqah Najiah Wan Hasan ◽  
Mohd Shukuri Mohamad Ali ◽  
Raja Noor Zaliha Raja Abdul Rahman ◽  
Abu Bakar Salleh ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Conformational Changes ◽  
Specific Activity ◽  
3D Structure ◽  
Coli Strain ◽  
Exchange Chromatography ◽  
Molecular Dynamic Simulations ◽  
Type I ◽  
Enzymatic Reactions ◽  
Dynamic Simulations

Genome mining revealed a 1011 nucleotide-long fragment encoding a type I L-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni(2+)-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni(2+) and Mg(2+), but it was inhibited by Mn(2+), Fe(3+) and Zn(2+) at the same concentration. J15 asparaginase actively hydrolysed its native substrate, l-asparagine, but had low activity towards l-glutamine. The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s(-1), and 4.21 s(-1) mM(-1), respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr₂₄ , His₂₂, Gly₂₃, Val₂₅ and Pro₂₆ may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment.

scholarly journals D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1072
Author(s):  
Alfredo Montes-Robledo ◽  
Rosa Baldiris-Avila ◽  
Johan Fabian Galindo
Keyword(s):  
Escherichia Coli ◽  
3D Structure ◽  
Pcr Amplification ◽  
Uropathogenic Escherichia Coli ◽  
Crystallographic Structure ◽  
Type I ◽  
Dynamic Simulations ◽  
Lectin Domain ◽  
In Silico Studies ◽  
Tract Infections

FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.

scholarly journals Functional Importance of Hydrophobic Patches on the Ebola Virus VP35 IFN-Inhibitory Domain

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2316
Author(s):  
Nodoka Kasajima ◽  
Keita Matsuno ◽  
Hiroko Miyamoto ◽  
Masahiro Kajihara ◽  
Manabu Igarashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ebola Virus ◽  
Structural Information ◽  
Site Directed Mutagenesis ◽  
Genome Replication ◽  
Type I ◽  
Multifunctional Protein ◽  
Functional Sites ◽  
Inhibitory Function ◽  
Inhibitory Domain

Viral protein 35 (VP35) of Ebola virus (EBOV) is a multifunctional protein that mainly acts as a viral polymerase cofactor and an interferon antagonist. VP35 interacts with the viral nucleoprotein (NP) and double-stranded RNA for viral RNA transcription/replication and inhibition of type I interferon (IFN) production, respectively. The C-terminal portion of VP35, which is termed the IFN-inhibitory domain (IID), is important for both functions. To further identify critical regions in this domain, we analyzed the physical properties of the surface of VP35 IID, focusing on hydrophobic patches, which are expected to be functional sites that are involved in interactions with other molecules. Based on the known structural information of VP35 IID, three hydrophobic patches were identified on its surface and their biological importance was investigated using minigenome and IFN-β promoter-reporter assays. Site-directed mutagenesis revealed that some of the amino acid substitutions that were predicted to disrupt the hydrophobicity of the patches significantly decreased the efficiency of viral genome replication/transcription due to reduced interaction with NP, suggesting that the hydrophobic patches might be critical for the formation of a replication complex through the interaction with NP. It was also found that the hydrophobic patches were involved in the IFN-inhibitory function of VP35. These results highlight the importance of hydrophobic patches on the surface of EBOV VP35 IID and also indicate that patch analysis is useful for the identification of amino acid residues that directly contribute to protein functions.

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