scholarly journals The Molecular Basis of Color Vision in Colorful Fish: Four Long Wave-Sensitive (LWS) Opsins in Guppies (Poecilia reticulata) are Defined by Amino Acid Substitutions at Key Functional Sites

2011 ◽  
pp. 231-256
Keyword(s):  
Amino Acid ◽  
Color Vision ◽  
Molecular Basis ◽  
Poecilia Reticulata ◽  
Amino Acid Substitutions ◽  
Functional Sites ◽  
Long Wave

scholarly journals Facilitating the Evolution of Esterase Activity from a Promiscuous Enzyme (Mhg) with Catalytic Functions of Amide Hydrolysis and Carboxylic Acid Perhydrolysis by Engineering the Substrate Entrance Tunnel

2016 ◽  
Vol 82 (22) ◽  
pp. 6748-6756 ◽  
Author(s):  
Xiaodan Yan ◽  
Jianjun Wang ◽  
Yu Sun ◽  
Junge Zhu ◽  
Sheng Wu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Engineering ◽  
Esterase Activity ◽  
Molecular Basis ◽  
Catalytic Triad ◽  
Amino Acid Substitutions ◽  
Biological Functions ◽  
Catalytic Activities ◽  
Efficient Strategy

ABSTRACTPromiscuous enzymes are generally considered to be starting points in the evolution of offspring enzymes with more specific or even novel catalytic activities, which is the molecular basis of producing new biological functions. Mhg, a typical α/β fold hydrolase, was previously reported to have both γ-lactamase and perhydrolase activities. However, despite having high structural similarity to and sharing an identical catalytic triad with an extensively studied esterase fromPseudomonas fluorescens, this enzyme did not show any esterase activity. Molecular docking and sequence analysis suggested a possible role for the entry of the binding pocket in blocking the entrance tunnel, preventing the ester compounds from entering into the pocket. By engineering the entrance tunnel with only one or two amino acid substitutions, we successfully obtained five esterase variants of Mhg. The variants exhibited a very broad substrate acceptance, hydrolyzing not only the classicalp-nitrophenol esters but also various types of chiral esters, which are widely used as drug intermediates. Site 233 at the entrance tunnel of Mhg was found to play a pivotal role in modulating the three catalytic activities by adjusting the size and shape of the tunnel, with different amino acid substitutions at this site facilitating different activities. Remarkably, the variant with the L233G mutation was a very specific esterase without any γ-lactamase and perhydrolase activities. Considering the amino acid conservation and differentiation, this site could be a key target for future protein engineering. In addition, we demonstrate that engineering the entrance tunnel is an efficient strategy to regulate enzyme catalytic capabilities.IMPORTANCEPromiscuous enzymes can act as starting points in the evolution of novel catalytic activities, thus providing a molecular basis for the production of new biological functions. In this study, we identified a critical amino acid residue (Leu233) at the entry of the substrate tunnel of a promiscuous enzyme, Mhg. We found that substitution of this residue with smaller amino acids such as Gly, Ala, Ser, or Pro endowed the enzyme with novel esterase activity. Different amino acids at this site can facilitate different catalytic activities. These findings exhibited universal significance in this subset of α/β fold hydrolases, including Mhg. Furthermore, we demonstrate that engineering the entrance tunnel is an efficient strategy to evolve new enzyme catalytic capabilities. Our study has important implications for the regulation of enzyme catalytic promiscuity and development of protein engineering methodologies.

Spectral-tuning mechanisms of marine mammal rhodopsins and correlations with foraging depth

2000 ◽  
Vol 17 (5) ◽  
pp. 781-788 ◽  
Author(s):  
JEFFRY I. FASICK ◽  
PHYLLIS R. ROBINSON
Keyword(s):  
Amino Acid ◽  
Marine Mammal ◽  
Molecular Basis ◽  
Marine Mammals ◽  
Visual Pigments ◽  
Amino Acid Substitutions ◽  
Spectral Tuning ◽  
Long Wavelength ◽  
Terrestrial Mammals ◽  
Deep Diving

It has been observed that deep-foraging marine mammals have visual pigments that are blue shifted in terms of their wavelength of maximal absorbance (λmax) when compared to analogous pigments from terrestrial mammals. The mechanisms underlying the spectral tuning of two of these blue-shifted pigments have recently been elucidated and depend on three amino acid substitutions (83Asn, 292Ser, and 299Ser) in dolphin rhodopsin, but only one amino acid substitution (308Ser) in the dolphin long-wavelength-sensitive pigment. The objective of this study was to investigate the molecular basis for changes in the spectral sensitivity of rod visual pigments from seven distantly related marine mammals. The results show a relationship between blue-shifted rhodopsins (λmax ≤ 490 nm), deep-diving foraging behavior, and the substitutions 83Asn and 292Ser. Species that forage primarily near the surface in coastal habitats have a rhodopsin with a λmax similar to that of terrestrial mammals (500 nm) and possess the substitutions 83Asp and 292Ala, identical to rhodopsins from terrestrial mammals.

scholarly journals Rifampin and Rifaximin Resistance in Clinical Isolates of Clostridium difficile

2008 ◽  
Vol 52 (8) ◽  
pp. 2813-2817 ◽  
Author(s):  
Jennifer R. O'Connor ◽  
Minerva A. Galang ◽  
Susan P. Sambol ◽  
David W. Hecht ◽  
Gayatri Vedantam ◽  
...  
Keyword(s):  
Amino Acid ◽  
Clostridium Difficile ◽  
Molecular Basis ◽  
Restriction Endonuclease Analysis ◽  
Clinical Isolates ◽  
Amino Acid Substitutions ◽  
Promising Alternative ◽  
Agar Dilution ◽  
Rifampin Resistance

ABSTRACT Rifaximin, a poorly absorbed rifamycin derivative, is a promising alternative for the treatment of Clostridium difficile infections. Resistance to this agent has been reported, but no commercial test for rifaximin resistance exists and the molecular basis of this resistance has not been previously studied in C. difficile. To evaluate whether the rifampin Etest would be a suitable substitute for rifaximin susceptibility testing in the clinical setting, we analyzed the in vitro rifaximin susceptibilities of 80 clinical isolates from our collection by agar dilution and compared these results to rifampin susceptibility results obtained by agar dilution and Etest. We found rifaximin susceptibility data to agree with rifampin susceptibility; the MICs of both antimicrobials for all isolates were either very low or very high. Fourteen rifaximin-resistant (MIC, ≥32 μg/ml) unique isolates from patients at diverse locations in three countries were identified. Molecular typing analysis showed that nine (64%) of these isolates belonged to the epidemic BI/NAP1/027 group that is responsible for multiple outbreaks and increased disease severity in the United Kingdom, Europe, and North America. The molecular basis of rifaximin and rifampin resistance in these isolates was investigated by sequence analysis of rpoB, which encodes the β subunit of RNA polymerase, the target of rifamycins. Resistance-associated rpoB sequence differences that resulted in specific amino acid substitutions in an otherwise conserved region of RpoB were found in all resistant isolates. Seven different RpoB amino acid substitutions were identified in the resistant isolates, which were divided into five distinct groups by restriction endonuclease analysis typing. These results suggest that the amino acid substitutions associated with rifamycin resistance were independently derived rather than disseminated from specific rifamycin-resistant clones. We propose that rifaximin resistance in C. difficile results from mutations in RpoB and that rifampin resistance predicts rifaximin resistance for this organism.

scholarly journals Recombinant Measles Viruses Expressing Altered Hemagglutinin (H) Genes: Functional Separation of Mutations Determining H Antibody Escape from Neurovirulence

2001 ◽  
Vol 75 (16) ◽  
pp. 7612-7620 ◽  
Author(s):  
Kerstin Moeller ◽  
Iain Duffy ◽  
Paul Duprex ◽  
Bert Rima ◽  
Rudi Beschorner ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Basis ◽  
Measles Virus ◽  
Escape Mutant ◽  
Amino Acid Substitutions ◽  
Structural Alterations ◽  
Recombinant Viruses ◽  
The Brain ◽  
H Protein

ABSTRACT Measles virus (MV) strain CAM/RB, which was adapted to growth in the brain of newborn rodents, is highly neurovirulent. It has been reported earlier that experimentally selected virus variants escaping from the monoclonal antibodies (MAbs) Nc32 and L77 to hemagglutinin (H) preserved their neurovirulence, whereas mutants escaping MAbs K71 and K29 were found to be strongly attenuated (U. G. Liebert et al., J. Virol. 68:1486–1493, 1994). To investigate the molecular basis of these findings, we have generated a panel of recombinant MVs expressing the H protein from CAM/RB and introduced the amino acid substitutions thought to be responsible for antibody escape and/or neurovirulence. Using these recombinant viruses, we identified the amino acid changes conferring escape from the MAbs L77 (377R→Q and 378M→K), Nc32 (388G→S), K71 (492E→K and 550S→P), and K29 (535E→G). When the corresponding recombinant viruses were tested in brains of newborn rodents, we found that the mutations mediating antibody escape did not confer differential neurovirulence. In contrast, however, replacement of two different amino acids, at positions 195G→R and 200S→N, which had been described for the escape mutant set, caused the change in neurovirulence. Thus, antibody escape and neurovirulence appear not to be associated with the same structural alterations of the MV H protein.

scholarly journals Amino Acid Substitutions in the S2 Region Enhance Severe Acute Respiratory Syndrome Coronavirus Infectivity in Rat Angiotensin-Converting Enzyme 2-Expressing Cells

2007 ◽  
Vol 81 (19) ◽  
pp. 10831-10834 ◽  
Author(s):  
Shuetsu Fukushi ◽  
Tetsuya Mizutani ◽  
Kouji Sakai ◽  
Masayuki Saijo ◽  
Fumihiro Taguchi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Acute Respiratory Syndrome ◽  
Angiotensin Converting Enzyme ◽  
Host Species ◽  
Molecular Basis ◽  
Amino Acid Substitutions ◽  
Converting Enzyme ◽  
S Protein ◽  
Angiotensin Converting Enzyme 2 ◽  
Virus Adaptation

ABSTRACT To clarify the molecular basis of severe acute respiratory syndrome coronavirus (SARS-CoV) adaptation to different host species, we serially passaged SARS-CoV in rat angiotensin-converting enzyme 2 (ACE2)-expressing cells. After 15 passages, the virus (Rat-P15) came to replicate effectively in rat ACE2-expressing cells. Two amino acid substitutions in the S2 region were found on the Rat-P15 S gene. Analyses of the infectivity of the pseudotype-bearing S protein indicated that the two substitutions in the S2 region, especially the S950F substitution, were responsible for efficient infection. Therefore, virus adaptation to different host species can be induced by amino acid substitutions in the S2 region.

scholarly journals The molecular basis of mouse adaptation by human enterovirus 71

2008 ◽  
Vol 89 (7) ◽  
pp. 1622-1632 ◽  
Author(s):  
Beng Hooi Chua ◽  
Patchara Phuektes ◽  
Sharon A. Sanders ◽  
Philip K. Nicholls ◽  
Peter C. McMinn
Keyword(s):  
Amino Acid ◽  
Capsid Protein ◽  
Cho Cells ◽  
Molecular Basis ◽  
Enterovirus 71 ◽  
Human Enterovirus ◽  
Amino Acid Substitutions ◽  
Single Mutation ◽  
Human Enterovirus 71 ◽  
Necrotizing Myositis

A mouse-adapted strain of human enterovirus 71 (HEV71) was selected by serial passage of a HEV71 clinical isolate (HEV71-26M) in Chinese hamster ovary (CHO) cells (CHO-26M) and in newborn BALB/c mice (MP-26M). Despite improved growth in CHO cells, CHO-26M did not show increased virulence in newborn BALB/c mice compared with HEV71-26M. By contrast, infection of newborn mice with MP-26M resulted in severe disease of high mortality. Skeletal muscle was the primary site of replication in mice for both viruses. However, MP-26M infection induced severe necrotizing myositis, whereas CHO-26M infection caused only mild inflammation. MP-26M was also isolated from whole blood, heart, liver, spleen and brain of infected mice. CHO-26M harboured a single mutation within the open reading frame (ORF), resulting in an amino acid substitution of K149→I in the VP2 capsid protein; two further ORF mutations that resulted in amino acid substitutions were identified in MP-26M, located within the VP1 capsid protein (G145→E) and the 2C protein (K216→R). Infectious cDNA clone-derived mutant virus populations containing the mutations identified in CHO-26M and MP-26M were generated in order to study the molecular basis of CHO cell and mouse adaptation. The VP2 (K149→I) change was responsible only for improved growth in CHO cells and did not lead to increased virulence in mice. Of the two amino acid substitutions identified in MP-26M, the VP1 (G145→E) mutation alone was sufficient to increase virulence in mice to the level observed in MP-26M-infected mice.

scholarly journals Amino Acid Substitutions in Transmembrane Domains 9 and 10 of GerVB That Affect the Germination Properties of Bacillus megaterium Spores

2008 ◽  
Vol 190 (24) ◽  
pp. 8009-8017 ◽  
Author(s):  
Graham Christie ◽  
Christopher R. Lowe
Keyword(s):  
Amino Acid ◽  
Bacillus Megaterium ◽  
Binding Sites ◽  
Molecular Basis ◽  
Transmembrane Domains ◽  
Site Directed Mutagenesis ◽  
Amino Acid Substitutions ◽  
Receptor Function ◽  
Outer Loop ◽  
Receptor Proteins

ABSTRACT The molecular basis for differences in germinant recognition of Bacillus megaterium QM B1551 spores containing the GerVB and/or GerUB receptor proteins has been examined by site-directed mutagenesis and the construction of cross-homologue chimeras. Focusing on nonconserved residues predicted to reside in transmembrane domains 9 and 10, we demonstrate that GerVB residues Ser319 and Leu345 are of particular importance in defining the specificity and apparent affinity of the receptor for germinants. Kinetic analyses of mutants with different amino acid substitutions at these positions indicate that Ser319 and Leu345 are not involved directly in the binding of germinants, but probably reside in regions of the receptor where structural perturbations can affect the conformation of, or access to, germinant binding sites. Position 345 is also shown to be of importance in GerUB, where the F345A mutation severely impairs receptor function. Functionality is restored in the GerUB Ala345 background by substituting putative outer-loop residues adjacent to TM10 for the corresponding residues in GerVB, indicating that a degree of structural coordination between these regions is important to receptor function.

Recombinant Variants of Tissue-Type Plasminogen Activator Containing Amino Acid Substitutions in the Finger Domain

1992 ◽  
Vol 68 (06) ◽  
pp. 672-677 ◽  
Author(s):  
Hitoshi Yahara ◽  
Keiji Matsumoto ◽  
Hiroyuki Maruyama ◽  
Tetsuya Nagaoka ◽  
Yasuhiro Ikenaka ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plasminogen Activator ◽  
Half Life ◽  
Tissue Type ◽  
Clot Lysis ◽  
Amino Acid Substitutions ◽  
Wild Type ◽  
Plasma Clot ◽  
Tissue Type Plasminogen Activator ◽  
Type Plasminogen Activator

SummaryTissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7–9, 10–14, 15–19, 28–33, and 37–42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37–42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37–42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37–42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37–42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.

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