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Protein
& Peptide Letters
ISSN: 0929-8665
Protein
& Peptide Letters
Volume 16, Number 10, 2009
Contents
Carboxylesterases: A World with Still Words
to Say
Guest Editor: Giuseppe Manco
Editorial Pp.
1135-1136
G. Manco
α/β
Hydrolase Fold: An Update Pp. 1137-1148
P.D. Carr and D.L. Ollis
[Abstract] [Purchase
Article]
Distinction Between Esterases and Lipases: Comparative
Biochemical Properties of Sequence-Related Carboxylesterases
Pp. 1149-1161
H. Chahinian and L. Sarda
[Abstract] [Purchase
Article]
Protein Engineering of Carboxyl Esterases by Rational
Design and Directed Evolution Pp. 1162-1171
M. Schmidt, D. Böttcher and U.T. Bornscheuer
[Abstract] [Purchase
Article]
Cold-Adapted Esterases and Lipases: From Fundamentals
to Application Pp. 1172-1180
M.L. Tutino, G. di Prisco, G. Marino and D. de
Pascale
[Abstract] [Purchase
Article]
Structure, Function and Applications of Carboxylesterases
from Insects for Insecticide Resistance Pp. 1181-1188
S. Yan, F. Cui and C. Qiao
[Abstract] [Purchase
Article]
Structural and Kinetic Overview of the Carboxylesterase
EST2 from Alicyclobacillus acidocaldarius: A Comparison
with the Other Members of the HSL Family Pp. 1189-1200
L. Mandrich, L. Merone and G. Manco
[Abstract] [Purchase
Article]
Conformational Stability of Esterase Enzymes from
Different Sources Pp. 1201-1206
P.D. Vecchio, G. Graziano and G. Barone
[Abstract] [Purchase
Article]
Human Carboxylesterases: An Update on CES1, CES2 and
CES3 Pp. 1207-1214
S.P. Sanghani, P.C. Sanghani, M.A. Schiel and W.F.
Bosron
[Abstract] [Purchase
Article]
Structure, Activities and Biomedical Applications
of Human Butyrylcholinesterase Pp. 1215-1224
P. Masson, E. Carletti and F. Nachon
[Abstract] [Purchase
Article]
Use of Esterase Activities for the Detection of Chemical
Neurotoxic Agents Pp. 1225-1234
G. Manco, R. Nucci and F. Febbraio
[Abstract] [Purchase
Article]
Production of Flavour Compounds from Fat During Cheese
Ripening by Action of Lipases and Esterases Pp. 1235-1243
I.V. Wolf, C.A. Meinardi and C.A. Zalazar
[Abstract] [Purchase
Article]
General Articles
Regular Papers
Glycosylation of Tetraspanin Tspan-1 at Four Distinct Sites
Promotes Its Transition Through the Endoplasmic
Reticulum Pp. 1244-1248
C.-J. Scholz, G. Sauer and H. Deissler
[Abstract] [Purchase
Article]
Characterisation of Oxidized Recombinant Human Galectin-1
Pp. 1249-1255
S.A. Scott, A. Bugarcic and H. Blanchard
[Abstract] [Purchase
Article]
Arginyl Aminopeptidase-Like 1 (RNPEPL1) Is an Alternatively
Processed Aminopeptidase with Specificity for Methionine,
Glutamine, and Citrulline Residues Pp. 1256-1266
M.W. Thompson, K.A. Beasley, M.D. Schmidt and
R.L. Seipelt
[Abstract] [Purchase
Article]
Evaluating Long-Term Relationship of Protein Sequence by Use
of D-Interval Conditional Probability
and Its Impact on Protein Structural Class Prediction Pp.
1267-1276
F. Gu and H. Chen
[Abstract] [Purchase
Article]
Abstracts
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Editorial
The study of carboxylesterases has received growing attention
in the last decades.
Several investigations have been performed in the second middle
of the last century when detection by in situ activity
staining on starch or acrylamide gels revealed the huge complexity,
in term of heterogeneity and micro heterogeneity, of this
group of enzymes [1]. It was soon clear that although easy
to visualise these enzymes escaped purification and therefore
a real in depth characterization. The complexity of patterns
and their straightforward production with inexpensive technologies
allowed scientists to propose them as a tool for classification
of species or assignment of specific cell types [2]. The idea
of protein profiling that nowadays is at the heart of proteomics
and biomarkers discovery was already there although in its
infancy. However, the low reproducibility of those patterns
impaired a more wide diffusion of this approach. With the
improvement of biochemical tools of protein analysis some
of these enzymes started to be purified and characterised,
mainly from those sources where a higher expression was obtained,
as for example in mammalian liver and in some microorganims
[3]. In particular, the presence in the liver made it possible
to propose a role in xenobiotic detoxification for these enzymes
[4]. In addition it was soon clear that carboxylesterases
are characterised by wide substrate specificity, which made
impossible a classification on this basis only. The understanding
that these were serine-type enzymes permitted the first attempt
to classify them on the basis of inhibitor sensitivity. Aldrige
in 1953 proposed the classification in A, B and C esterases,
with A esterases not inhibited by paraoxon and able to degrade
it, B esterases were defined as those strongly inhibited by
paraoxon and C esterases were not inhibited but unable to
degrade the pesticide [5]. However, studies at that time did
not made a lot of progress due to low expression of the enzymes
and the presence of many different activities, which made
purification and detailed characterization difficult.
Figure 1. Papers retrieved from PubMed (www.ncbi.nlm.nih.gov/)
in the period 1960-2008 by using the term “carboxylesterase”.
With the advent of the technology of recombinant DNA the study
of carboxylesterases received a substantial boost. It was
possible to clone the genes, to express the enzymes in bacteria
and purify them quite easily, also thanks to further technological
improvement. Finally, the overall genome sequencing of several
species gave a clearer picture of the distribution of these
enzymes, their phylogenetic relationships and functional importance.
By looking at the number of papers that today appear by browsing
the PubMed database with the term “carboxylesterase”
as keyword ranging from 1960 to 2008, it is evident that starting
from the 1980s there was a substantial increase in the number
of published papers with a burst in this decade thanks to
the proteomics era. If we look at the number of sequences
that are filed in the ESTER database http//bioweb.ensam.inra.fr/ESTHER/general?what=index)
we are impressed by the wide diffusion of these enzymes in
all domains of life and in all environments suggesting some
important roles in cellular survival and adaptation. However,
most of the importance of these enzymes and of their strict
cousins “lipases” comes from their use as biocatalysts
in chemical reactions. Being hydrolytic enzymes which lack
cofactor requirement and being endowed with a wide specificity
several esterases have found application in fine chemicals
synthesis and in other fields although their potentialities
are still underestimated.
The scope of this special issue of Protein and Peptide Letters
is to give a broad overview of different aspects of carboxylesterases
ranging from fold, to classification, to structure/function
studies of enzymes from different sources and finally to applications,
such as in the field of biosensors, pesticides decontamination
and flavour development in cheese. Several specialists in
this field agreed to participate in this effort and their
contribution is gratefully acknowledged. We also thanks scientists
that declined the invitation and apologise with those could
have been invited but are not in this issue due to space limitations.
All things considered I believe that the final result is really
valuable and that this issue of Protein and Peptide Letters
will give to the readers a good panoramic of this world that
have still words to say.
REFERENCES:
[1] Augustinsson, K. B. (1961) Ann. N.E:
Acad. Sci., 94, 844.
[2] Lung, G. (1965) J. Gen. Microbiol.,
40, 413.
[3] Manco, G., Di Gennaro, S., De Rosa M. and Rossi M. (1994)
Eur. J. Biochem., 221, 965.
[4] Heymann, E. & Mentlein, R. (1981)
Carboxylesterases amidases, Methods Enzymol., 77,
533.
[5] Aldridge, W. N. (1953) Biochem. J.,
53, 110.
Giuseppe Manco
Guest Editor
Protein & Peptide Letters
Institute of Protein Biochemistry (IBP)
National Research Council (CNR)
Via Pietro Castellino 111
80131, Naples
Italy
E-mail: g.manco@ibp.cnr.it
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Article]
α/β
Hydrolase Fold: An Update
P.D. Carr and D.L. Ollis
The α/β
hydrolase superfamily has rapidly expanded in recent years
and continues to do so at an expeditious pace. According to
the ESTHER database (http://bioweb.ensam.inra.fr/ESTHER) 29000
papers have been published cataloguing 89 family groups, comprising
a total of 15438 gene loci and 666 structures. This paper
presents a snapshot of the current family taxonomy, catalytic
chemistries, structural topologies and useful technologies
emerging from the knowledge base at the current time.
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Article]
Distinction Between Esterases and Lipases: Comparative
Biochemical Properties of Sequence-Related Carboxylesterases
H. Chahinian and L. Sarda
Carboxylesterases (Carboxyl ester hydrolase) include two groups
of enzymes, namely non-specific esterases (EC 3.1.1.1) and
lipases (EC 3.1.1.3) which have been early differentiated
on the basis of their substrate specificity. Esterases hydrolyse
solutions of water-soluble short acyl chain esters and are
inactive against water-insoluble long chain triacylglycerols
which, in turn, are specifically hydrolyzed by lipases. Based
on the comparison of the primary structures, three families
of sequence-related carboxylesterases, namely the lipoprotein
lipase family (L-family), the hormone-sensitive lipase family
(H-family) and the cholinesterase family (C-family) have been
identified. Using solutions and emulsions of vinyl, glyceryl
and p-nitrophenyl esters, we have reinvestigated the kinetic
properties of some esterases and lipases of the H- and C-families.
Results indicate that esterases and lipases, which are both
active on soluble esters, can be differentiated by their value
of Km. Moreover, esterase, unlike lipases, are inactive against
water-insoluble esters as vinyl laurate and trioctanoylglycerol.
From the the comparison of structural features of sequence-related
esterases and lipases, it appears that lipases, unlike esterases,
display a significant difference in the distribution of hydrophobic
amino acid residues at vicinity of their active site. This
observation supports the hypothesis of the existence in lipases
of a particular surface domain that specifically interacts
with lipid-water interfaces and contributes to the transfer
a single substrate molecule from the organized lipid-water
interface (supersubstrate) to the catalytic site of the enzyme.
[Back to top]
[Purchase
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Protein Engineering of Carboxyl Esterases by Rational
Design and Directed Evolution
M. Schmidt, D. Böttcher and U.T.
Bornscheuer
In the past few years a considerable number of mutagenesis
methods and high-throughput screening (HTS) systems have been
developed and improved. In parallel, computer programs or
software packages for molecular modeling have been further
investigated. Thus, the number of examples for successful
directed evolution and rational design is increasing constantly.
In this review the essential mutagenesis methods and HTS systems,
especially for esterases, are described and various examples
for the application of these protein engineering tools are
provided.
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[Purchase
Article]
Cold-Adapted Esterases and Lipases: From Fundamentals
to Application
M.L. Tutino, G. di Prisco, G. Marino and D. de
Pascale
Micro-organisms that thrive at low temperatures produce
cold-adapted enzymes which display high catalytic efficiency,
generally associated with low thermal stability. In the recent
past, researchers and industries have focused the attention
on cold-adapted enzymes, whose peculiar properties make them
particularly interesting either for investigating stability/flexibility
relationships, or for their potential application in industrial
processes. Among these enzymes, lipases and esterases, have
potential utilisations in a broad range of biotechnological
applications. In fact, these biocatalysts represent the most
widely used enzymes in biotechnology and organic chemistry.
Modern methods of genetic engineering combined with growing
knowledge of structure and function allow further adaptation
to industrial needs and exploration of novel applications.
Hence, in this review we attempt to offer an overview on some
psychrophilic esterases and lipases; major details will be
presented for ORF PSHAa0051 from Pseudoalteromonas haloplanktis
TAC125, recently investigated by our team. In addition, potential
biotechnological applications will be discussed.
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Structure, Function and Applications of Carboxylesterases
from Insects for Insecticide Resistance
S. Yan, F. Cui and C. Qiao
Carboxylesterases (EC 3.1.1.1) distribute broadly
in insects, and play an important role in the metabolism with
various functions. This paper reviews the insect carboxylesterases
including the definitions and reaction mechanism, classification,
structural context, functions especially on insecticide resistance,
and its application.
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Article]
Structural and Kinetic Overview of the Carboxylesterase
EST2 from Alicyclobacillus acidocaldarius: A Comparison
with the Other Members of the HSL Family
L. Mandrich, L. Merone and G. Manco
Thermophilic and hyperthermophilic carboxylesterases (EC 3.1.1.1)
are excellent model systems for studying structure function
relationships as well as in vitro and in vivo
evolution and possible biotechnological applications. In this
paper we review the main aspect of one of most studied microbial
representative of the hormone sensitive lipase family (HSL),
namely carboxylesterase 2 (EST2) from Alicyclobacillus
acidocaldarius.
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Article]
Conformational Stability of Esterase Enzymes from
Different Sources
P.D. Vecchio, G. Graziano and G. Barone
In the last years we have performed a series of studies
to characterize the conformational stability of three esterases
from thermophilic and mesophilic sources: Aes esterase from
Escherichia coli, EST2 from Alicyclobacillus
acidocaldarius and AFEST from Archeoglobus fulgidus.
These three esterases belong to the Hormone-sensitive lipase
group of the superfamily of carboxylester hydrolases. The
conformational stability of the three enzymes against temperature,
urea and GuHCl has been determined by means of circular dichroism,
fluorescence and differential scanning calorimetry measurements.
Analysis of experimental data coupled with available structural
information allowed us to suggest that the optimization of
charge-charge interactions on the protein surface could be
one of the mechanisms to increase the thermal stability for
the three esterases. This idea has been tested in the case
of EST2, which shows a fully reversible thermal unfolding,
by producing and studying variant forms of wild type enzyme
in which a charged residue has been mutated. In the present
article the obtained results are critically recollected in
order to provide a clear and unified scenario.
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Human Carboxylesterases: An Update on CES1, CES2 and
CES3
S.P. Sanghani, P.C. Sanghani, M.A. Schiel and W.F.
Bosron
Carboxylesterases belong to Phase I group of drug
metabolizing enzymes. They hydrolyze a variety of drug esters,
amides, carbamates and similar structures. There are five
‘carboxylesterase’ genes listed in the Human Genome
Organization database. In this review, we will focus on the
CES1, CES2 and CES3 genes and their protein products that
have been partially characterized. Several variants of these
three CESs result from alternate splicing, single nucleotide
polymorphisms and multiple copy variants. The three CESs,
are largely localized to tissues that are major sites of drug
metabolism like the mucosa of the gastrointestinal tract,
lungs and liver but, they differ in tissue-specific expression.
The amino acid alignment of the three CESs reveals important
conserved catalytic and structural residues. There are interesting
insertions and deletions that may affect enzymatic function
as determined by homology modeling of CES3 using the CES1
three-dimensional structure. A comparison of the substrate
specificity of CES1 versus CES2 reveals broad but distinct
substrate preferences. There is little information on the
substrate specificity of CES3 but it seems to have a lower
catalytic efficiency than the other two CESs for selected
substrates.
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Structure, Activities and Biomedical Applications
of Human Butyrylcholinesterase
P. Masson, E. Carletti and F. Nachon
Human butyrylcholinesterase (BuChE) is a serine enzyme present
in most organs and plasma. No clear physiological function
has yet been assigned to BuChE, but it is a pharmacologically
and toxicologically important enzyme that plays a role in
degradation of numerous ester-containing drugs and poisonous
esters. Thus, BuChE-based bioscavengers are an alternative
for prophylaxis and treatments of intoxications by these compounds.
Also, BuChE has been integrated in biosensors for detection
of organophosphorus compounds and other cholinesterase inhibitors.
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Use of Esterase Activities for the Detection of Chemical
Neurotoxic Agents
G. Manco, R. Nucci and F. Febbraio
The quest for a quick and easy detection of the neurotoxin
levels in the environment has fostered the search for systems
alternative to currently employed analytical methods such
as spectrophotometry, gas–liquid chromatography, thin-layer
chromatography, and more recently mass spectrometry. These
drawbacks lead to intense research efforts to develop biosensor
devices for the determination of these compounds. In this
review, we present an overview of the actual development of
research in neurotoxin detection by using enzymatic biosensors
based on esterase activity, in particular cholinesterases,
and carboxylesterases. Detection by enzymatic activity could
be carried out measuring the hydrolysis products or the residual
enzymatic activity after inhibition, using a transducer system
that makes possible the correlation between the determined
activity and the analyte concentration. Several transducer
systems were adopted for the neurotoxins identification using
esterases, including electrochemical, optical, conductimetric
and piezoelectric procedures. The differences in the used
transducer determine the final sensitivity and specificity
of the biosensor. Moreover, a brief description of immobilization
procedure, that is an important step in the biosensor development
and could affect the final characteristic of biosensor (sensibility,
stability, response time and reproducibility), was accomplished.
Final considerations on advantages and problems, related to
actual development of these technologies, and its prospective
were discussed.
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Production of Flavour Compounds from Fat During Cheese
Ripening by Action of Lipases and Esterases
I.V. Wolf, C.A. Meinardi and C.A. Zalazar
The milk fat is an essential component for the development
of correct flavour in cheese. The lipolysis and catabolism
of fatty acids are two biochemical events very important on
flavour development of some cheese varieties. The role and
characteristics of various lipolytic agents during cheese
ripening is reviewed and discused.
Before starting with the specific study about formation of
flavour compounds from milk fat during cheese ripening, a
brief review of the technological aspects of cheese production
is needed.
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Glycosylation of Tetraspanin Tspan-1 at Four Distinct Sites
Promotes Its Transition Through the Endoplasmic
Reticulum
C.-J. Scholz, G. Sauer and H. Deissler
We showed that Tspan-1, a tetraspanin overexpressed in
many human cancers, harbours oligosaccharides at all four
potential N-glycosylation sites. Its most abundant form contained
only mannose-rich sugar chains but two distinct glycosylation
sites could also contain complex carbohydrates. Glycosylation
seemed to be required for correct folding and subsequent transition
through the endoplasmic reticulum.
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Characterisation of Oxidized Recombinant Human Galectin-1
S.A. Scott, A. Bugarcic and H. Blanchard
Oxidized human galectin-1 plays a role in the immune response
to injured axons. Over-expression of galectin-1 by cancer,
in combination with cancer associated oxidative stress suggests
oxidized human galectin-1 may also play a role(s) in tumourigenesis.
Here we generate milligram quantities of oxidized human galectin-1
and undertake biophysical characterization. The protein adopts
a number of different states. Two separable oxidized forms
are identified that exist as largely mono-disperse solutions
at higher milligram/ml concentrations. The presence of disulphide
bonds is confirmed for these two protein forms, as is their
change in overall shape and loss of lectin activity. Our studies
lead to production of a particular mono-disperse oxidized
human galectin-1 species that is anticipated most optimal
for investigations requiring milligram/ml concentrations such
as X-ray crystallography.
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Arginyl Aminopeptidase-Like 1 (RNPEPL1) Is an Alternatively
Processed Aminopeptidase with Specificity for Methionine,
Glutamine, and Citrulline Residues
M.W. Thompson, K.A. Beasley, M.D. Schmidt and
R.L. Seipelt
A previously uncharacterized member of the M1 family of
zinc metallopeptidases, arginyl aminopeptidase-like 1 (RNPEPL1;
EC 3.4.11.1), was cloned and expressed, and the recombinant
enzyme characterized. RNPEPL1 was a broad specificity aminopeptidase
with preference for a P1 methionine, glutamine, or citrulline
residue, and exhibited a broad pH preference, with maximal
activity observed between pH 6.6 and 8.0. The enzyme was inhibited
by calcium ions but unaffected by chloride ions, and was insensitive
to specific inhibitors of the closely-related arginyl aminopeptidase,
indicating similarity to leukotriene A4
hydrolase. RT-PCR analysis of RNPEPL1 expression revealed
a ubiquitous tissue distribution, consistent with a general
housekeeping function, but also revealed alternative splicing
of the mRNA in all tissues examined. The inclusion of intron
5 was predicted to result in a truncated protein product,
while an alternative 3’ splice site of exon 9 of the
reference sequence was predicted to result in the omission
of a conserved eleven amino acid stretch from the C-terminal
domain.
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Evaluating Long-Term Relationship of Protein Sequence by Use
of D-Interval Conditional Probability and Its Impact on Protein
Structural Class Prediction
F. Gu and H. Chen
To fix the large and expanding gap between sequence known
proteins and structure known proteins, it is important to
study on protein structural class prediction (PSCP) for its
foundation and usefulness in protein structure analysis. In
this paper, the d-interval conditional probability index was
proposed to reflect the long-term correlation between amino
acids. Based on this index, the impact of residues’
long-term relationship on PSCP was analyzed. Two new information
theory based algorithms were proposed and were used combining
with the long-term information between residues to predict
protein structural class (PSC). The dataset 5714 was tested
for its low sequence similarity and high reliability. The
result showed that the new index was 3-6% higher than traditional
index by use of the same algorithms, and the PSCP accuracy
was 4-10% improved using the new algorithms. The presented
index, algorithms and the long-term relationship of residues
on PSCP can be extensively applied in other sequence based
protein structure analysis.
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