scholarly journals Biochemical Analysis of Phytolacca DOPA Dioxygenase

2015 ◽  
Vol 10 (5) ◽  
pp. 1934578X1501000
Author(s):  
Kana Takahashi ◽  
Kazuko Yoshida ◽  
Kei Yura ◽  
Hiroshi Ashihara ◽  
Masaaki Sakuta
Keyword(s):  
Biochemical Analysis ◽  
Structural Model ◽  
Specific Activity ◽  
Three Dimensional ◽  
Single Amino Acid ◽  
Phytolacca Americana ◽  
Conserved Motif ◽  
Single Amino Acid Residue ◽  
The Difference

The biochemical analysis of Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) was carried out. The recombinant protein of PaDOD1 catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. While the reported motif conserved in DODs from betalain-producing plants was found in PaDOD1, a single amino acid residue alteration was detected in PaDOD2. A mutated PaDOD1 protein with a change of 177 Asn to Gly showed reduced specific activity compared with PaDOD1, while DOPA dioxygenase activity was not observed for a mutated PaDOD2 protein which had its conserved motif replaced with that of PaDOD1. A three-dimensional (3D) structural model of PaDOD1 and PaDOD2 showed that the conserved motif in DODs was located in the N-terminal side of a loop, which was found close to the putative active site. The difference in stability of the loop may affect the enzymatic activity of PaDOD2.

scholarly journals Differences in a Single Extracellular Residue Underlie Adhesive Functions of Two Zebrafish Aqp0s

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2005
Author(s):  
Irene Vorontsova ◽  
James E. Hall ◽  
Thomas F. Schilling ◽  
Noriaki Nagai ◽  
Yosuke Nakazawa
Keyword(s):  
Cell Adhesion ◽  
Single Amino Acid ◽  
Amino Acid Difference ◽  
Adhesion Assay ◽  
Loss Of Function ◽  
Adhesive Properties ◽  
The Difference ◽  
In Vitro Adhesion ◽  
Cell To Cell Adhesion

Aquaporin 0 (AQP0) is the most abundant lens membrane protein, and loss of function in human and animal models leads to cataract formation. AQP0 has several functions in the lens including water transport and adhesion. Since lens optics rely on strict tissue architecture achieved by compact cell-to-cell adhesion between lens fiber cells, understanding how AQP0 contributes to adhesion would shed light on normal lens physiology and pathophysiology. We show in an in vitro adhesion assay that one of two closely related zebrafish Aqp0s, Aqp0b, has strong auto-adhesive properties while Aqp0a does not. The difference appears to be largely due to a single amino acid difference at residue 110 in the extracellular C-loop, which is T in Aqp0a and N in Aqp0b. Similarly, P110 is the key residue required for adhesion in mammalian AQP0, highlighting the importance of residue 110 in AQP0 cell-to-cell adhesion in vertebrate lenses as well as the divergence of adhesive and water permeability functions in zebrafish duplicates.

scholarly journals Role of the reaction-structure coupling in temperature compensation of the KaiABC circadian rhythm

2021 ◽  
Author(s):  
Masaki Sasai
Keyword(s):  
Temperature Compensation ◽  
Oscillation Amplitude ◽  
Thermal Fluctuations ◽  
Reaction Rates ◽  
System Level ◽  
Single Amino Acid ◽  
Structural Transitions ◽  
Single Amino Acid Residue ◽  
Residue Substitution

When the mixture solution of cyanobacterial proteins, KaiA, KaiB, and KaiC, is incubated with ATP in vitro, the phosphorylation level of KaiC shows stable oscillations with the temperature-compensated circadian period. We analyzed this temperature compensation by developing a theoretical model describing the feedback relations among reactions and structural transitions in the KaiC molecule. The model showed that the reduced structural cooperativity should weaken the negative feedback coupling among reactions and structural transitions, which enlarges the oscillation amplitude and period, explaining the observed significant period extension upon single amino-acid residue substitution. We propose that an increase in thermal fluctuations similarly attenuates the reaction-structure feedback, explaining the temperature compensation in the KaiABC clock. The model suggests that the ATPase reactions in the CI domain of KaiC affect the period depending on how the reaction rates are modulated. The KaiABC clock provides a unique opportunity to analyze how the reaction-structure coupling regulates the system-level synchronized oscillations of molecules.

scholarly journals A single amino acid change converts Aurora-A into Aurora-B-like kinase in terms of partner specificity and cellular function

2009 ◽  
Vol 106 (17) ◽  
pp. 6939-6944 ◽  
Author(s):  
Jingyan Fu ◽  
Minglei Bian ◽  
Junjun Liu ◽  
Qing Jiang ◽  
Chuanmao Zhang
Keyword(s):  
Amino Acid ◽  
Aurora Kinase ◽  
Single Amino Acid ◽  
Aurora B ◽  
Aurora A ◽  
Single Amino Acid Residue ◽  
Single Amino Acid Change ◽  
Equivalent Residue ◽  
And Function

Aurora kinase-A and -B are key regulators of the cell cycle and tumorigenesis. It has remained a mystery why these 2 Aurora kinases, although highly similar in protein sequence and structure, are distinct in subcellular localization and function. Here, we report the striking finding that a single amino acid residue is responsible for these differences. We replaced the Gly-198 of Aurora-A with the equivalent residue Asn-142 of Aurora-B and found that in HeLa cells, Aurora-AG198N was recruited to the inner centromere in metaphase and the midzone in anaphase, reminiscent of the Aurora-B localization. Moreover, Aurora-AG198N compensated for the loss of Aurora-B in chromosome misalignment and cell premature exit from mitosis. Furthermore, Aurora-AG198N formed a complex with the Aurora-B partners, INCENP and Survivin, and its localization depended on this interaction. Aurora-AG198N phosphorylated the Aurora-B substrates INCENP and Survivin in vitro. Therefore, we propose that the presence of Gly or Asn at a single site assigns Aurora-A and -B to their respective partners and thus to their distinctive subcellular localizations and functions.

Study on overlapping of two sequential scans in laser forming

2007 ◽  
Vol 221 (9) ◽  
pp. 993-997 ◽  
Author(s):  
H Shen ◽  
J Zhou ◽  
Z Q Yao
Keyword(s):  
Plastic Strain ◽  
Material Properties ◽  
Structural Model ◽  
Three Dimensional ◽  
High Strength ◽  
Laser Beams ◽  
Laser Forming ◽  
Numerical Investigations ◽  
Localized Heating ◽  
The Difference

Laser forming can utilize localized heating for the forming of high strength alloys and use combinations of straightandcurved lines to produce three-dimensional formedcomponents, which are of significant value to industries of aerospace, shipbuilding, and microelectronics. A three-dimensional non-linear, indirectly coupled thermal—structural model for the overlapping ratio of two sequential laser beams scanning is established, accounting for temperature dependency of material properties. Numerical results are verified by experimental data. Numerical investigations are carried out to examine the difference in plastic strain distributions under different overlapping ratios. The results show that the bending angle is larger when the size of plastic zone on the top surface is wider, although the plastic strain is smaller.

scholarly journals Fine Molecular Tuning of Chimeric Antigen Receptors through Hinge Length Optimization

2020 ◽  
Author(s):  
Scott McComb ◽  
Tina Nguyen ◽  
Kevin A. Henry ◽  
Darin Bloemberg ◽  
Susanne Maclean ◽  
...  
Keyword(s):  
Amino Acid ◽  
Growth Factor ◽  
Epidermal Growth Factor ◽  
Specific Activity ◽  
Single Amino Acid ◽  
Single Domain Antibody ◽  
Normal Tissues ◽  
Epidermal Growth

AbstractBackgroundChimeric antigen receptor (CAR) technology has revolutionized the treatment of B-cell malignancies and steady progress is being made towards CAR-immunotherapies for solid tumours. In the context of CARs targeting antigens which are commonly overexpressed in cancer but also expressed at lower levels in normal tissues, such as epidermal growth factor family receptors EGFR or HER2, it is imperative that any targeting strategy consider the potential for on-target off-tumour toxicity. Molecular optimization of the various protein domains of CARs can be used to increase the tumour selectivity.MethodHerein, we utilize high-throughput CAR screening to identify a novel camelid single-domain antibody CAR (sdCAR) targeting human epidermal growth factor (EGFR) with high EGFR-specific activity. To further optimize the target selectivity of this EGFR-sdCAR, we performed progressive N-terminal single amino acid truncations of an extended human CD8 hinge domain [(G4S)3GG-45CD8h] to improve selectivity for EGFR-overexpressing cells. We also make direct comparison of varying hinge domains in scFv-based CARs targeting EGFR-family tumour associated antigens EGFRvIII and HER2.ResultsThrough comparison of various hinge-truncated scFv- and sdAb-based CARs, we show that the CAR hinge/spacer domain plays varying roles in modifying CAR signaling depending upon target epitope location. For membrane-proximal epitopes, hinge truncation by even a single amino acid resulted in fine control of CAR signaling strength. Hinge-modified CARs showed consistent and predictable signaling in Jurkat-CAR cells and primary human CAR-T cells in vitro and in vivo.ConclusionsOverall, these results indicate that membrane-proximal epitope targeting CARs can be optimized through hinge length tuning for improved target selectivity and therapeutic function. Graphical Abstract

scholarly journals Homology Modeling-Based in Silico Affinity Maturation Improves the Affinity of a Nanobody

2019 ◽  
Vol 20 (17) ◽  
pp. 4187 ◽  
Author(s):  
Xin Cheng ◽  
Jiewen Wang ◽  
Guangbo Kang ◽  
Min Hu ◽  
Bo Yuan ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Rational Design ◽  
Structural Model ◽  
Three Dimensional ◽  
Phage Display Library ◽  
Affinity Maturation ◽  
New Strategy ◽  
Design Protocol ◽  
High Binding Affinity

Affinity maturation and rational design have a raised importance in the application of nanobody (VHH), and its unique structure guaranteed these processes quickly done in vitro. An anti-CD47 nanobody, Nb02, was screened via a synthetic phage display library with 278 nM of KD value. In this study, a new strategy based on homology modeling and Rational Mutation Hotspots Design Protocol (RMHDP) was presented for building a fast and efficient platform for nanobody affinity maturation. A three-dimensional analytical structural model of Nb02 was constructed and then docked with the antigen, the CD47 extracellular domain (CD47ext). Mutants with high binding affinity are predicted by the scoring of nanobody-antigen complexes based on molecular dynamics trajectories and simulation. Ultimately, an improved mutant with an 87.4-fold affinity (3.2 nM) and 7.36 °C higher thermal stability was obtained. These findings might contribute to computational affinity maturation of nanobodies via homology modeling using the recent advancements in computational power. The add-in of aromatic residues which formed aromatic-aromatic interaction plays a pivotal role in affinity and thermostability improvement. In a word, the methods used in this study might provide a reference for rapid and efficient in vitro affinity maturation of nanobodies.

scholarly journals Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11570
Author(s):  
Chhavi Sharma ◽  
Arti Nigam ◽  
Rajni Singh
Keyword(s):  
Structure Function ◽  
Bacillus Cereus ◽  
Structural Model ◽  
Three Dimensional ◽  
Conformational Space ◽  
Dimensional Structure ◽  
After Effects ◽  
Short Life Span ◽  
Therapeutic Enzymes

Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.

scholarly journals The Capsid Proteins of Aleutian Mink Disease Virus Activate Caspases and Are Specifically Cleaved during Infection

2009 ◽  
Vol 84 (6) ◽  
pp. 2687-2696 ◽  
Author(s):  
Fang Cheng ◽  
Aaron Yun Chen ◽  
Sonja M. Best ◽  
Marshall E. Bloom ◽  
David Pintel ◽  
...  
Keyword(s):  
Virus Infection ◽  
Disease Virus ◽  
Virus Production ◽  
Capsid Proteins ◽  
Single Amino Acid ◽  
Aleutian Mink Disease Virus ◽  
Single Amino Acid Residue ◽  
Caspase 7

ABSTRACT Aleutian mink disease virus (AMDV) is currently the only known member of the genus Amdovirus in the family Parvoviridae. It is the etiological agent of Aleutian disease of mink. We have previously shown that a small protein with a molecular mass of approximately 26 kDa was present during AMDV infection and following transfection of capsid expression constructs (J. Qiu, F. Cheng, L. R. Burger, and D. Pintel, J. Virol. 80:654-662, 2006). In this study, we report that the capsid proteins were specifically cleaved at aspartic acid residue 420 (D420) during virus infection, resulting in the previously observed cleavage product. Mutation of a single amino acid residue at D420 abolished the specific cleavage. Expression of the capsid proteins alone in Crandell feline kidney (CrFK) cells reproduced the cleavage of the capsid proteins in virus infection. More importantly, capsid protein expression alone induced active caspases, of which caspase-10 was the most active. Active caspases, in turn, cleaved capsid proteins in vivo. Our results also showed that active caspase-7 specifically cleaved capsid proteins at D420 in vitro. These results suggest that viral capsid proteins alone induce caspase activation, resulting in cleavage of capsid proteins. We also provide evidence that AMDV mutants resistant to caspase-mediated capsid cleavage increased virus production approximately 3- to 5-fold in CrFK cells compared to that produced from the parent virus AMDV-G at 37°C but not at 31.8°C. Collectively, our results indicate that caspase activity plays multiple roles in AMDV infection and that cleavage of the capsid proteins might have a role in regulating persistent infection of AMDV.

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