Strategy for Polymorphic Control by Enzymatic Reaction and Antisolvent Crystallization: Effect of Aminoacylase on Metastable β-Glycine Formation

2021 ◽  
Author(s):  
Jen-Chieh Hsueh ◽  
Kuan Lin Yeh ◽  
Hung Lin Lee ◽  
Tu Lee
Keyword(s):  
Amino Acid ◽  
Enzymatic Reaction ◽  
Amino Acid Polymorphism ◽  
Enantioselective Resolution ◽  
Long Time ◽  
Antisolvent Crystallization ◽  
Crystallization Effect

Although the enantioselective resolution by aminoacylase has been established for a long time, the effect of aminoacylase on the amino acid polymorphism is still unclear. To explore whether the presence...

The assessment of density functionals for DNA–protein stacked and T-shaped complexes

2010 ◽  
Vol 88 (8) ◽  
pp. 815-830 ◽  
Author(s):  
Lesley R. Rutledge ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acid ◽  
Potential Energy ◽  
Large Scale ◽  
Enzymatic Reaction ◽  
Basis Sets ◽  
Density Functionals ◽  
Interaction Energies ◽  
Π Interactions ◽  
Hybrid Techniques ◽  
Semi Empirical

The present work uses 129 nucleobase – amino acid CCSD(T)/CBS stacking and T-shaped interaction energies as reference data to test the ability of various density functionals with double-zeta quality basis sets, as well as some semi-empirical and molecular mechanics methods, to accurately describe noncovalent DNA–protein π–π and π+–π interactions. The goal of this work is to identify methods that can be used in hybrid approaches (QM/MM, ONIOM) for large-scale modeling of enzymatic systems involving active-site (substrate) π–π contacts. Our results indicate that AMBER is a more appropriate choice for the lower-level method in hybrid techniques than popular semi-empirical methods (AM1, PM3), and suggest that AMBER accurately describes the π–π interactions found throughout DNA–protein complexes. The M06–2X and PBE-D density functionals were found to provide very promising descriptions of the 129 nucleobase – amino acid interaction energies, which suggests that these may be the most suitable methods for describing high-level regions. Therefore, M06–2X and PBE-D with both the 6–31G(d) and 6–31+G(d,p) basis sets were further examined through potential-energy surface scans to better understand how these techniques describe DNA–protein π–π interactions in both minimum and nonminimum regions of the potential-energy surfaces, which is critical information when modeling enzymatic reaction pathways. Our results suggest that studies of stacked nucleobase – amino acid systems should implement the PBE-D/6–31+G(d,p) method. However, if T-shaped contacts are involved and (or) smaller basis sets must be considered due to limitations in computational resources, then M06–2X/6–31G(d) provides an overall excellent description of both nucleobase – amino acid stacking and T-shaped interactions for a range of DNA–protein π–π and π+–π interactions.

scholarly journals A 13-mer peptide straddling the leucine33/proline33 polymorphism in glycoprotein IIIa does not define the PLA1 epitope

Blood ◽  
1991 ◽  
Vol 77 (9) ◽  
pp. 1964-1969 ◽  
Author(s):  
F Flug ◽  
R Espinola ◽  
LX Liu ◽  
C SinQuee ◽  
R DaRosso ◽  
...  
Keyword(s):  
Amino Acid ◽  
Polyclonal Antibodies ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Adenosine Diphosphate ◽  
Enzyme Linked Immunosorbent Assay ◽  
Amino Acid Polymorphism ◽  
Glycoprotein Iiia ◽  
Polymerase Chain ◽  
Induced Aggregation

Abstract We confirm the recent report (J Clin Invest 83:1778, 1989) of a polymorphism at amino acid 33 of platelet GPIIIa associated with the PLA1/PLA2 phenotype by using the polymerase chain reaction on cDNA derived from platelet RNA, using the base-pair primers 105–129 and 452- 428. Platelet cDNA from three PLA2-homozygous individuals, when digested with Nci I, gave two bands of 256 bp and 91 bp, whereas eight PLA1 cDNAs gave a single band of 347 bp. Two 13-mer amino acid peptides straddling the amino acid polymorphism: SDEALP (L/P) GSPRCD were synthesized for epitope studies. Two mouse polyclonal antibodies were raised: one against the PLA1-associated peptide, the other against the PLA2 peptide. Both antibodies react with either peptide, as well as with both PLA1 and PLA2 platelets. The PLA1 peptide did not block the binding of two different human anti-PLA1 antibodies to the 100-Kd GPIIIa band on immunoblot of platelet extracts; neither did it block the binding of the same antibodies to PLA1-platelet extracts in an enzyme-linked immunosorbent assay. Further studies were performed on the PLA1 epitope following subtilisin digestion of purified GPIIIa. A 55-Kd fragment was obtained that retained the PLA1 epitope as well as the first 13 N-terminal amino acids of GPIIIa. Reduction of the 55-Kd fragment resulted in loss of the PLA1 epitope with production of a 67- Kd, 21-Kd, and 10-Kd band on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The 55-Kd band does not react with LK-2, a monoclonal antibody versus GPIIIa that inhibits adenosine diphosphate, collagen, epinephrine, and thrombin-induced aggregation. Thus, the PLA1 epitope is conformation-induced, resides on an N-terminal 55-Kd fragment composed of two or more peptides held together by -SH bonds, and is not required for platelet aggregation.

scholarly journals Effect of single amino acid substitutions on the formation of the PlA and Bak alloantigenic epitopes

Blood ◽  
1991 ◽  
Vol 78 (3) ◽  
pp. 681-687 ◽  
Author(s):  
A Goldberger ◽  
M Kolodziej ◽  
M Poncz ◽  
JS Bennett ◽  
PJ Newman
Keyword(s):  
Amino Acid ◽  
Expression System ◽  
Single Amino Acid ◽  
Expression Vectors ◽  
Membrane Glycoproteins ◽  
Amino Acid Polymorphism ◽  
Specific Expression ◽  
Mammalian Expression ◽  
Single Amino Acid Polymorphisms ◽  
Necessary And Sufficient

Abstract The subunits that comprise the platelet-specific integrin alpha IIb beta 3 are polymorphic in nature, with several allelic forms present in the human gene pool. Minor changes in the secondary and tertiary structures of platelet membrane glycoproteins (GP) IIb and IIIa encoded by these alleles can result in an alloimmune reaction after transfusion or during pregnancy. To better understand the molecular structure of the PlA alloantigen system, located on GPIIIa, and the Bak alloantigen on GPIIb, we used a heterologous mammalian expression system to express these integrin subunits in their known polymorphic forms. An expression vector containing the PlA1 form of a GPIIIa cDNA, which encodes a leucine at amino acid 33 (Leu33), was modified to express the PlA2- associated form encoding a proline at amino acid 33 (Pro33). Similarly, a Baka GPIIb cDNA expressing an isoleucine at amino acid 843 (IIe843) was modified to express the Bakb form containing a serine at the same position (Ser843). Transfection of these vectors into COS cells resulted in the synthesis of GPIIb and GPIIIa molecules that were identical in size to those present in platelet lysates. Immunoprecipitation of the GPIIIa-transfected COS lysates with PlA)- specific alloantisera indicated that the Leu33 form was recognized only by anti-PIA1 sera while the Pro33 form was bound only by anti-PlA2 sera, showing that single amino acid polymorphisms are necessary and sufficient to direct the formation of the PlA1 and PlA2 alloepitopes. Similar experiments with Bak allele-specific expression vectors indicated that while the amino acid polymorphism (IIe843 in equilibrium Ser843) was necessary, posttranslational processing of pro-IIb was required for efficient exposure of both the Baka and Bakb alloepitopes.

Three new components contained in the vitelline coat of Tegula pfeifferi

Zygote ◽  
1999 ◽  
Vol 8 (S1) ◽  
pp. S61-S61 ◽  
Author(s):  
Kazu Haino-Fukushima ◽  
Xuxi Fan ◽  
Shouka Nakamura
Keyword(s):  
Amino Acids ◽  
Polyacrylamide Gel Electrophoresis ◽  
Enzymatic Reaction ◽  
Base Pairs ◽  
Sulphated Polysaccharides ◽  
Reading Frame ◽  
Glycosylation Sites ◽  
Long Time ◽  
Protein Components ◽  
Vitelline Coat

The vitelline coat (VC) lysin of Tegula, a marine molluscan genus, is released from the acrosome of sperm during fertilisation and can lyse the VC of only the same species. The lytic action of this lysin against the VC is not an enzymatic reaction, but a stoichiometric and irreversible one (Haino-Fukushima, 1974).The VC of Tegula pfeifferi consists of glycoproteins containing sulphated polysaccharides, which account for roughly two-thirds of the entire weight of the VC. The presence of a large quantity of polysaccharides in the VC had prevented rapid progress in the analysis of its protein components. Last year, we succeeded in a complete solubilisation of the VC by boiling for a long time in 1% SDS solution, and determined the cDNA sequence coding for a mature 41 kDa glycoprotein, which appears to be the major component of the VC from the results of SDS-polyacrylamide gel electrophoresis (PAGE). The cDNA, referred to as vcp41, comprises 1072 base pairs and contains one open reading frame with a sequence for 319 amino acids containing 19 amino acids of a signal peptide. The deduced amino acid sequence has five N-glycosylation sites and ten cysteine residues. It seems that almost 7 kDa in this 41kDa glycoprotein is polysaccharide constituents (Fan & Haino-Fukushima, 1998).

scholarly journals An amino acid polymorphism in the couch potato gene forms the basis for climatic adaptation in Drosophila melanogaster

2008 ◽  
Vol 105 (42) ◽  
pp. 16207-16211 ◽  
Author(s):  
P. S. Schmidt ◽  
C.-T. Zhu ◽  
J. Das ◽  
M. Batavia ◽  
L. Yang ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Amino Acid ◽  
Amino Acid Polymorphism ◽  
Climatic Adaptation

Serine/alanine amino acid polymorphism of the L-cone photopigment assessed by dual Rayleigh-type color matches

1994 ◽  
Vol 34 (3) ◽  
pp. 377-382 ◽  
Author(s):  
Elizabeth Sanocki ◽  
Steven K. Shevell ◽  
Joris Winderickx
Keyword(s):  
Amino Acid ◽  
Amino Acid Polymorphism

Cefotaxime-Resistant EnterobacteriaceaeIsolates from a Hospital in Warsaw, Poland: Identification of a New CTX-M-3 Cefotaxime-Hydrolyzing β-Lactamase That Is Closely Related to the CTX-M-1/MEN-1 Enzyme

1998 ◽  
Vol 42 (4) ◽  
pp. 827-832 ◽  
Author(s):  
Marek Gniadkowski ◽  
Ines Schneider ◽  
Andrzej Pal/ucha ◽  
Renate Jungwirth ◽  
Barbara Mikiewicz ◽  
...  
Keyword(s):  
Amino Acid ◽  
Clinical Laboratory ◽  
Amino Acid Sequences ◽  
Hospital Environment ◽  
M Gene ◽  
E Coli ◽  
Men 1 ◽  
Long Time ◽  
Dna Restriction ◽  
Tract Infections

ABSTRACT A group of cefotaxime-resistant Citrobacter freundiiand Escherichia coli isolates were collected by a clinical laboratory in a hospital in Warsaw, Poland, in July 1996. Detailed analysis has shown that all of these produced a β-lactamase (pI, 8.4) belonging to the CTX-M family, one of the minor extended-spectrum β-lactamase families with a strong cefotaxime-hydrolyzing activity. Sequencing has revealed that C. freundii isolates produced a new CTX-M-3 enzyme which is very closely related to the CTX-M-1/MEN-1 β-lactamase, sporadically identified in Europe over a period of 6 years. Amino acid sequences of these two β-lactamases differ at four positions: Val77Ala, Asp114Asn, Ser140Ala, and Asn288Asp (the first amino acid of each pair refers to CTX-M-1/MEN-1 and second refers to CTX-M-3). The partial sequence of the E. coli CTX-M gene was identical to the corresponding region ofbla CTX-M-3, but a transconjugant of theE. coli isolate expressed higher levels of resistance to β-lactams than did C. freundii transconjugants. These resistance differences correlated with differences in plasmid DNA restriction patterns. Our results suggest that CTX-M genes have been spread among different species of the familyEnterobacteriaceae in the hospital and that the CTX-M-3-expressing C. freundii strain causing routine urinary tract infections has been maintained for a relatively long time in the hospital environment.

scholarly journals A single amino acid polymorphism in the glycosyltransferase CpsK defines four Streptococcus suis serotypes

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
David Roy ◽  
Taryn B. T. Athey ◽  
Jean-Philippe Auger ◽  
Guillaume Goyette-Desjardins ◽  
Marie-Rose Van Calsteren ◽  
...  
Keyword(s):  
Amino Acid ◽  
Streptococcus Suis ◽  
Single Amino Acid ◽  
Amino Acid Polymorphism ◽  
Single Amino Acid Polymorphism
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