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Current
Protein & Peptide Science
ISSN: 1389-2037
Upcoming Articles
The Retinal cGMP Phosphodiesterase γ-Subunit
— A Chameleon
Lian-Wang Guo and Arnold E. Ruoho
[Abstract]
Into the Lipid Realm: Stability and Thermodynamics
of Membrane Proteins
Francisco N. Barrera, Luis A. Alcaraz, Estefanía
Hurtado-Gómez and José L. Neira,
[Abstract]
Advances and Pitfalls in Protein Structure Prediction
D. Cozzetto and A. Tramontano
[Abstract]
Flexible Structures and Ligand Interactions of Tandem
Repeats Consisting of Proline, Glycine, Asparagine, Serine,
and/or Threonine Rich Oligopeptides in Proteins
Norio Matsushima, Hitoshi Yoshida, Yasuhiro Kumaki,
Masakatsu Kamiya, Takanori Tanaka, Yoshinobu Izumi and
Robert H. Kretsinger
[Abstract]
Plasma Gelsolin: Function, Prognostic Value, and Potential
Therapeutic Use
Robert Bucki, Ilya Levental, Alina Kulakowska and
Paul A. Janmey
[Abstract]
Thermal Adaptation of Heat Shock Proteins
A. Muga and F. Moro
[Abstract]
Relaxin and Nitric Oxide Signalling
M.C. Baccari and D. Bani
[Abstract]
The Importance of Being Flexible: The Case of Basic Region
Leucine Zipper Transcriptional Regulators
Maria Miller
[Abstract]
The Classic Basic Protein of Myelin – Conserved Structural
Motifs and the Dynamic Molecular Barcode Involved in Membrane
Adhesion and Protein-Protein Interactions
George Harauz and David S. Libich
[Abstract]
Quality Assessment of Protein Structure Models
Daisuke Kihara, Hao Chen and Yifeng David
Yang
[Abstract]
Focus on Phosphoarginine and Phospholysine
P.G. Besant, P.V. Attwood and M.J. Piggott
[Abstract]
Methods for Calculating the Entropy and Free Energy and their
Application to Problems Involving Protein Flexibility and
Ligand Binding
Hagai Meirovitch, Srinath Cheluvaraja, and
Ronald P. White
[Abstract]
The Importance of Being Flexible: The Case of Basic Region
Leucine Zipper Transcriptional Regulators
Maria Miller
[Abstract]
Solvent Viscosity and Friction in Protein Folding Dynamics
Stephen J. Hagen
[Abstract]
The Role of Thiols and Disulfides on Protein Stability in
Formulations
Maulik V. Trivedi, Jennifer S. Laurence, and
Teruna J. Siahaan
[Abstract]
A Guide to Template Based Structure Prediction
Xiaotao Qu, Rosemarie Swanson, Ryan Day and Jerry
Tsai
[Abstract]
Predicting Affinity and Specificity of Antigenic Peptide Binding
to Major Histocompatibility Class I Molecules
Florian Sieker, Andreas May and Martin Zacharias
[Abstract]
Extracellular Proteases as Targets for Drug Development
Mare Cudic and Gregg B. Fields
[Abstract]
Molecular and Biotechnological Advances in Milk Proteins in
Relation to Human Health
Jagat R. Kanwara, Rupinder K. Kanwar , Xueying
Sunb, Vasu Punj, H. Matta, Somasundaram M. Morley, Andrew
Parratt, Munish Purif and Rakesh Sehgal
[Abstract]
Linking New Paradigms in Protein Chemistry to Reversible Membrane
Protein Interactions
Øyvind Halskau, Arturo Muga and Aurora
Martínez
[Abstract]
Metallothioneins and Cancer
Tomas Eckschlager, Vojtech Adam, Jan Hrabeta, Katarina Figova
and Rene Kizek
[Abstract]
Quantitative Investigation of Biomolecular Interactions in
Crowded Media by Fluorescence Spectroscopy, a Good Choice
Silvia Zorrilla and M. Pilar Lillo
[Abstract]
Diverse Roles of GADD45α
in Stress Signaling
Ming Gao, Ning Guo, Chuanshu Huang and Lun Song
[Abstract]
Abstracts
[Back to top]
The Retinal cGMP Phosphodiesterase γ-Subunit
— A Chameleon
Lian-Wang Guo and Arnold E. Ruoho
Intrinsically disordered proteins (IDPs) represent an emerging
class of proteins (or domains) that are characterized by a
lack of ordered secondary and tertiary structure. This group
of proteins has recently attracted tremendous interest primarily
because of a unique feature: they can bind to different targets
due to their structural plasticity, and thus fulfill diverse
functions. The inhibitory γ-subunit
(PDE?) of retinal PDE6 is an intriguing IDP, of which unique
protein properties are being uncovered. PDEγ
critically regulates the turn on as well as the turn off of
visual signaling through alternate interactions with the PDE6
catalytic core, transducin, and the regulator of G protein
signaling RGS9-1. The intrinsic disorder of PDEγ
does not compromise, but rather, optimizes its functionality.
PDEγ“curls
up” when free in solution but “stretches out”
when binding with the PDE6 catalytic core. Conformational
changes of PDEγ
also likely occur in its C-terminal PDE6-binding region upon
interacting with transducin during PDE6 activation. Growing
evidence shows that PDEγ
is also a player in non-phototransduction pathways, suggesting
additional protein targets. Thus, PDEγ
is highly likely to be adaptive in its structure and function,
hence a “chameleon”.
[Back to top]
Into the Lipid Realm: Stability and Thermodynamics
of Membrane Proteins
Francisco N. Barrera, Luis A. Alcaraz, Estefanía
Hurtado-Gómez and José L. Neira,
The first comprehensive studies on the structure and
thermodynamics of membrane proteins have started revealing
the exact architecture of these macromolecules and the physical-chemical
rules behind their structures. In this review, the stabilities
of several families of membrane proteins, obtained by using
spectroscopic, calorimetric and single molecule techniques
are surveyed. The data on the stability of membrane proteins
are compared with those obtained in soluble proteins. The
comparison indicates that although the number of particular
atomic interactions is larger in membrane proteins than in
soluble ones, the overall values are similar. The consensus
is that some intrinsic properties of membrane proteins resemble
those of soluble ones, but there are critical differences
arising form the inter-molecular contacts with the surrounding
membrane. Taken together, all these efforts improve our understanding
of the universal forces governing protein folding, and will
help in the design of membrane proteins in the near future.
[Back to top]
Advances and Pitfalls in Protein Structure Prediction
D. Cozzetto and A. Tramontano
Three dimensional protein structures are crucial for understanding
biology at both molecular and system level. Despite the advances
in experimental structural biology, the pace of sequence deposition
into databanks considerably exceeds that of structure determination.
Inevitably the functional annotation of genes and genomes
requires the exploitation of bioinformatics methods for protein
sequence comparison and structure prediction. Hence monitoring
objectively the state of art of the field is of paramount
importance, in order to make best use of computational protein
models to address biological questions. This review describes
some relevant issues in the field of structural bioinformatics,
emphasizig both open basic questions and the progress being
continuously achieved. It is reasonably expected that these
bioinformatics methods will increasingly contribute to the
biomedical, pharmaceutical and biotechnological research.
[Back to top]
Flexible Structures and Ligand Interactions of Tandem
Repeats Consisting of Proline, Glycine, Asparagine, Serine,
and/or Threonine Rich Oligopeptides in Proteins
Norio Matsushima, Hitoshi Yoshida, Yasuhiro Kumaki,
Masakatsu Kamiya, Takanori Tanaka, Yoshinobu Izumi
and Robert H. Kretsinger
Tandem repeats occur in 14% of all proteins. The repeat
unit lengths range from a single amino acid to more than 100
residues and the repeat number is sometimes over 100. Understanding
the structures, functions, and evolution of these repeats
is a significant goal in both proteomics and genomics. This
review summarizes experimental studies addressing structural
features of tandem repeats of short oligopeptides that are
rich in proline, glycine, asparagine, serine, and/or threonine.
The oligopetides include (PGMG) and (PNN) in biomineralization
protein (PM27), and (NPNA) in Plasmodium falciparum
circumsporozoite protein, (YSPTSPS) in RNA polymerase II,
(PHGGGWGQ) in the prion protein, (YGHGGG(N)) and (YNHGGG(G))
in plant glycine-rich proteins, (PGQGQQ), (PGQGQQGQQ) and
(GYYPTSOQQ) of wheat HMW glutenin, (FGGMGGGKGG) in Aequipecten
abductin. Spectroscopic studies including NMR and CD indicate
that these peptides adopt type I and II β-turns,
polyproline II helices, loop conformations, and random coils.
Formation of these structures frequently depends on pH, solvent,
temperature and hydration. The loop conformations are sometimes
stabilized by cation-π,
CH-π,
and/or amino-aromatic interactions. These observations indicate
that many tandem repeats are largely flexible. In addition
to generating repeating domains and providing flexible linkers
between domains, the tandem repeats of (PHGGGWGQ), (YGHGGG(N))
and (YNHGGG(G)) and those in titin bind Cu2+
ions; whereas, tandem repeats of (NPNA) and those in elastin
bind Ca2+ ions. The interactions
of some tandem repeats with various target proteins probably
involve an induced fit. The tandem repeats in tropoelastin,
flagelliform silk, wheat HMW glutenin, abductin, titin, and
human nucleoporin, nup153, are responsible for elastomeric
properties.
[Back to top]
Plasma Gelsolin: Function, Prognostic Value, and Potential
Therapeutic Use
Robert Bucki, Ilya Levental, Alina Kulakowska and
Paul A. Janmey
Gelsolin is a highly conserved, multifunctional
actin-binding protein initially described in the cytosol of
macrophages and subsequently identified in many vertebrate
cells. A unique property of gelsolin is that in addition to
its widely recognized function as a cytoplasmic regulator
of actin organization, the same gene expresses a splice variant
coding for a distinct isoform, plasma gelsolin, which is secreted
into extracellular fluids. The secreted form of gelsolin has
been implicated in a number of processes such as the extracellular
actin scavenging system and the presentation of lysophosphatidic
acid and other inflammatory mediators to their receptors,
in addition to its function as a substrate for extracellular
matrix-modulating enzymes. Consistent with these proposed
functions, blood gelsolin levels decrease markedly in a variety
of clinical conditions such as acute respiratory distress
syndrome, sepsis, major trauma, prolonged hyperoxia, malaria,
and liver injury. This correlation between blood gelsolin
levels and critical clinical conditions suggests the potential
utility of gelsolin as a prognostic marker as well as the
possibility for therapeutic replenishment of gelsolin to alleviate
the injurious cascades in these settings. This review summarizes
current data supporting a role of plasma gelsolin in extracellular
fluids and the potential for its use as a diagnostic marker
or therapeutic treatment in several medical conditions.
[Back to top]
Thermal Adaptation of Heat Shock Proteins
A. Muga and F. Moro
Heat shock proteins (Hsps) are molecular chaperones
that oppose stress-induced denaturation of other proteins.
Hsps are present in all organisms. Apart from assisting in
the efficient folding of newly synthesized proteins they maintain
pre-existing proteins in a stable conformation, preventing
their aggregation, under stress conditions. The latter role,
essential for thermal adaptation, requires that the chaperone
system change from a folding to a storing function at heat
shock temperatures. The temperature at which this change occurs
depends on the presence of a thermosensor in at least one
of the components of the chaperone systems. In this review,
we focus on the bacterial GroE and DnaK systems, describe
their temperature-sensitive protein components, and the location
of the thermosensor within the structure of these components.
While the thermosensor of the GroE system is located at the
inter-ring interface of GroEL, that of the DnaK system occurs
in its co-chaperone GrpE. Analysis of these examples demonstrates
the amazing mechanistic diversity of thermal stress adaptation
and of functional convergence of structurally unrelated proteins.
[Back to top]
Relaxin and Nitric Oxide Signalling
M.C. Baccari and
D. Bani
The peptide hormone relaxin (RLX) has been
shown to exert a variety of functions in both reproductive
and non-reproductive tissues. The molecular mechanism of RLX
on its target cells appears to involve multiple intracellular
signalling systems, including the nitric oxide (NO) pathway.
NO is an ubiquitous molecule synthesised from L-arginine under
the catalytic action of different nitric oxide synthase (NOS)
isoforms and its altered production has been reported to be
involved in several diseases. RLX has been demonstrated to
promote NO biosynthesis by up-regulating NOS expression; its
influence on the different NOS appears to depend on the cell
type studied. In addition to its physiological roles, RLX
has been postulated as a potential therapeutic agent in several
diseases. In particular, based on its property to promote
NO biosynthesis, RLX may be regarded as a therapeutic tool
in diseases characterized pathogenically by an impaired NO
production. The aim of the present mini-review is to summarize
and discuss the pathophysiological actions of RLX, strictly
related to its ability to activate the endogenous NO pathway
in reproductive and non-reproductive target organs.
[Back to top]
The Importance of Being Flexible: The Case of
Basic Region Leucine Zipper Transcriptional Regulators
Maria Miller
Large volumes of protein sequence and structure
data acquired by proteomic studies led to the development
of computational bioinformatic techniques that made possible
the functional annotation and structural characterization
of proteins based on their primary structure. It has become
evident from genome-wide analyses that many proteins in eukaryotic
cells are either completely disordered or contain long unstructured
regions that are crucial for their biological functions. The
content of disorder increases with evolution indicating a
possibly important role of disorder in the regulation of cellular
systems. Transcription factors are no exception and several
proteins of this class have recently been characterized as
premolten/molten globules. Yet, mammalian cells rely on these
proteins to control expression of their 30,000 or so genes.
Basic region:leucine zipper (bZIP) DNA-binding proteins constitute
a major class of eukaryotic transcriptional regulators. This
review discusses how conformational flexibility “built”
into the amino acid sequence allows bZIP proteins to interact
with a large number of diverse molecular partners and to accomplish
their manifold cellular tasks in a strictly regulated and
coordinated manner.
[Back to top]
The Classic Basic Protein of Myelin – Conserved Structural
Motifs and the Dynamic Molecular Barcode Involved in Membrane
Adhesion and Protein-Protein Interactions
George Harauz and David S. Libich
The myelin basic protein (MBP) family comprises a variety
of developmentally-regulated members arising from different
transcription start sites, differential splicing, and post-translational
modifications. The “classic” isoforms of MBP include
the 18.5 kDa form, which predominates in adult human myelin
and facilitates compaction of the mature myelin sheath in
the central nervous system, thereby maintaining its structural
integrity. In addition to membrane-association, the 18.5 kDa
and all other classic isoforms are able to interact with a
multitude of proteins, including Ca2+-calmodulin,
actin, tubulin, and SH3-domain containing proteins, and thus
may be signalling linkers during myelin development and remodelling.
All proteins in this family are intrinsically disordered,
creating a large effective surface to facilitate multiple
protein associations, and are post-translationally modified
to various degrees by methylation, phosphorylation, and deimination.
We have used spectroscopic (fluorescence, CD, EPR, and NMR)
approaches to study MBP’s conformational adaptability.
A highly-conserved central domain presents an amphipathic
α-helix
in association with a phospholipid membrane, and contains
a threonyl residue that is phosphorylated by MAP-kinases.
In multiple sclerosis, this segment represents a primary immunodominant
epitope. This helical structure is adjacent to a proline-rich
region that presents a classic SH3-ligand, comprises a second
MAP-kinase phosphorylation site, and forms a polyproline type
II helix. This domain of the protein is thus essential to
proper positioning of a protein-interaction motif, with the
local conformation and accessibility being modulated by MAP-kinases.
In addition, the C-terminus of 18.5 kDa MBP has been identified
by NMR spectroscopy as a Ca2+-calmodulin-binding
site, and is of note for having a high density of post-translational
modifications (protein kinase C phosphorylation, and deimination).
For the most part, any classic protein isoform functions as
an entropic spring that interacts in its entirety with membranes
and cytoskeletal proteins, but the central and C-terminal
motifs may represent molecular switches.
[Back to top]
Quality Assessment of Protein Structure Models
Daisuke Kihara, Hao Chen and Yifeng David
Yang
Computational protein tertiary structure prediction has
made significant progress over the last decade due to the
advancement of techniques and the growth of sequence and structure
databases. However, it is still not very easy to predict the
accuracy of a given predicted structure. Predicting the accuracy,
or quality assessment of a prediction model, is crucial for
a practical use of the model such as biochemical experimental
design and drug design. Recently several model quality assessment
programs (MQAPs) have been proposed for assessing global and
local accuracy of predicted structures. We will start with
reviewing the current status of protein structure prediction
methods with an emphasis on the source of errors. Then existing
MQAPs are classified into several categories and each is discussed.
The categories include methods which evaluate the quality
of template-target alignments, those which evaluate stereochemical
irregularities of prediction models, and methods which integrate
several features into a composite quality assessment score.
[Back to top]
Focus on Phosphoarginine and Phospholysine
P.G. Besant, P.V. Attwood and M.J. Piggott
Protein phosphorylation is a common signaling mechanism
in both prokaryotic and eukaryotic organisms. Whilst serine,
threonine and tyrosine phosphorylation dominate much of the
literature there are several other amino acids that are phosphorylated
in a variety of organisms. Two of these phosphoamino acids
are phosphoarginine and phospholysine. This review will focus
on the chemistry and biochemistry of both phosphoarginine
and ≅phospholysine. In particular we focus on the biological
aspects of ≅phosphoarginine as a means of storing and
using metabolic energy (in ≅place of phosphocreatine
in invertebrates), the chemistry behind ≅its synthesis
and we examine the chemistry behind its high-energy phosphoramidate
bond. In addition we will be reporting on the incidence of
phosphoarginine in mammalian cells. Similarly we will be ≅reviewing
the current findings on the biology and the chemistry of ⇓phospholysine
and its involvement in a variety of biological systems.
[Back to top]
Methods for Calculating the Entropy and Free Energy and their
Application to Problems Involving Protein Flexibility and
Ligand Binding
Hagai Meirovitch, Srinath Cheluvaraja, and Ronald
P. White
The Helmholtz free energy, F and the entropy,
S are related thermodynamic quantities with a special
importance in structural biology. We describe the difficulties
in calculating these quantities and review recent methodological
developments. Because protein flexibility is essential for
function and ligand binding, we discuss the related problems
involved in the definition, simulation, and free energy calculation
of microstates (such as the α-helical
region of a peptide). While the review is broad, a special
emphasize is given to methods for calculating the absolute
F (S), where our HSMC(D) method is described in some
detail.
[Back to top]
The Importance of Being Flexible: The Case of Basic Region
Leucine Zipper Transcriptional Regulators
Maria Miller
Large volumes of protein sequence and structure data acquired
by proteomic studies led to the development of computational
bioinformatic techniques that made possible the functional
annotation and structural characterization of proteins based
on their primary structure. It has become evident from genome-wide
analyses that many proteins in eukaryotic cells are either
completely disordered or contain long unstructured regions
that are crucial for their biological functions. The content
of disorder increases with evolution indicating a possibly
important role of disorder in the regulation of cellular systems.
Transcription factors are no exception and several proteins
of this class have recently been characterized as premolten/molten
globules. Yet, mammalian cells rely on these proteins to control
expression of their 30,000 or so genes. Basic region:leucine
zipper (bZIP) DNA-binding proteins constitute a major class
of eukaryotic transcriptional regulators. This review discusses
how conformational flexibility “built” into the
amino acid sequence allows bZIP proteins to interact with
a large number of diverse molecular partners and to accomplish
their manifold cellular tasks in a strictly regulated and
coordinated manner.
[Back to top]
Solvent Viscosity and Friction in Protein Folding Dynamics
Stephen J. Hagen
The famous Kramers rate theory for diffusion-controlled
reactions has been extended in numerous ways and successfully
applied to many types of reactions. Its application to protein
folding reactions has been of particular interest in recent
years, as many researchers have performed experiments and
simulations to test whether folding reactions are diffusion-controlled,
whether the solvent is the source of the reaction friction,
and whether the friction-dependence of folding rates generally
can provide insight into folding dynamics. These experiments
involve many practical difficulties, however. They have also
produced some unexpected results. Here we briefly review the
Kramers theory for reactions in the presence of strong friction
and summarize some of the subtle problems that arise in the
application of the theory to protein folding. We discuss how
the results of these experiments ultimately point to a significant
role for internal friction in protein folding dynamics. Studies
of friction in protein folding, far from revealing any weakness
in Kramers theory, may actually lead to new approaches for
probing diffusional dynamics and energy landscapes in protein
folding.
[Back to top]
The Role of Thiols and Disulfides on Protein Stability in
Formulations
Maulik V. Trivedi, Jennifer S. Laurence, and
Teruna J. Siahaan
There has been a tremendous increase in the number of
approved drugs derived from recombinant proteins; however,
their development as potential drugs has been hampered by
their instability that causes difficulty to formulate them
as therapeutic agents. It has been shown that the reactivity
of thiol and disulfide functional groups could catalyze chemical
(i.e., oxidation and beta-elimination reactions)
and physical (i.e., aggregation and precipitation)
degradations of proteins. Because most proteins contain a
free Cys residue or/and a disulfide bond, this review is focused
on their roles in the physical and chemical stability of proteins.
The effect of introducing a disulfide bond to improve physical
stability of proteins and the mechanisms of degradation of
disulfide bond were discussed. The qualitative/quantitative
methods to determine the presence of thiol in the Cys residue
and various methods to derivatize thiol group for improving
protein stability were also illustrated.
[Back to top]
A Guide to Template Based Structure Prediction
Xiaotao Qu, Rosemarie Swanson, Ryan Day and
Jerry Tsai
Template based protein structure prediction (commonly
referred to as homology or comparative modeling) uses knowledge
of solved structures to model a protein sequence’s native
or true fold. First, a parent structure is found and then
a template structure is built by mapping the target sequence
onto the parent structure. This putative structure is refined
using a combination of backbone moves, side-chain packing,
and loop modeling. Template based protein structure prediction
has always held great promise to produce atomically accurate
models close to the native conformation based on two major
assumptions. First, similar sequences exhibit similar protein
folds. Second, soluble proteins populate a discrete fold space
with many representatives already solved in our Protein Data
Bank (PDB). Ironically, beginning so close to the native structure
is also the primary source of problems confronting this method
and is the reason for the lack of progress in this category
of structure prediction. In this review, the general concepts
and procedures for template based structure prediction are
outlined based on the following topics: sequence alignment,
parent structure selection, template structure building, refinement,
evaluation, and final structure selection. Then, a description
of established software and algorithms is provided where the
advantages and limitations of the different methods will be
pointed out. This is followed by a discussion of the developments
in template based structure prediction up to the 7th
Critical Assessment of Structure Prediction meeting. Lastly,
we will address the increased difficulty in improving templates
that start so close to the native structure, and discuss the
improvements needed in this field.
[Back to top]
Predicting Affinity and Specificity of Antigenic
Peptide Binding to Major Histocompatibility Class I Molecules
Florian Sieker, Andreas May and
Martin Zacharias
Major Histo-Compatibility (MHC) class I molecules
are major agents of the mammalian adaptive immune system.
Class I molecules bind short antigenic peptides with a length
of 8-10 residues in the Endoplasmatic Reticulum (ER) and after
transport to the cell surface the peptides are presented to
T-lymphocytes. The binding site of class I molecules is formed
by a deep cleft between two α-helices
at top of an extended β-sheet.
Only tightly bound high-affinity peptides have a chance to
reach the cell surface and trigger an immune response. It
is therefore of great interest to identify possible high-affinity
antigenic peptides that could be used as vaccines to help
the immune system to detect viral infections or kill malignant
cells. A large number of crystal structures of antigenic peptides
in complex with class I alleles have been determined that
allow to understand the structural details important for peptide
binding. Biophysical and biochemical analysis of peptide-class
I complexes has resulted in a number of rules concerning the
selection of high-affinity peptides. However, an accurate
prediction of allele specific peptide-binding is still not
possible. This issue is currently addressed by various computational
tools developed by the bioinformatics community. The computational
efforts range from statistical analysis of peptide motifs
stored in databases to application of neural network methods
and support vector machine approaches. In addition, structure
based approaches to predict class I binding specificity including
molecular modeling and molecular dynamics (MD) simulations
will also be presented.
[Back to top]
Extracellular Proteases as Targets for Drug Development
Mare Cudic and Gregg B. Fields
Proteases constitute one of the primary targets in drug
discovery. In the present review, we focus on extracellular
proteases (ECPs) because of their differential expression
in many pathophysiological processes, including cancer, cardiovascular
conditions, and inflammatory, pulmonary, and periodontal diseases.
Many new ECP inhibitors are currently under clinical investigation
and a significant increase in new therapies based on protease
inhibition can be expected in the coming years. In addition
to directly blocking the activity of a targeted protease,
one can take advantage of differential expression in disease
states to selectively deliver therapeutic or imaging agents.
Recent studies in targeted drug development for the metalloproteases
(matrix metalloproteinases, adamalysins, pappalysins, neprilysin,
angiotensin-converting enzyme, metallocarboxypeptidases, and
glutamate carboxypeptidase II), serine proteases (elastase,
coagulation factors, tissue/urokinase plasminogen activator
system, kallikreins, tryptase, dipeptidyl peptidase IV) and
cysteine proteases (cathepsin B) are discussed herein.
[Back to top]
Molecular and Biotechnological Advances in Milk Proteins
in Relation to Human Health
Jagat R. Kanwara, Rupinder K. Kanwar , Xueying
Sunb, Vasu Punj, H. Matta, Somasundaram M. Morley, Andrew
Parratt, Munish Purif and Rakesh Sehgal
Milk and colostrum is a rich source of proteins/peptides
which have crucial roles in both neonates and adults. Milk
bioactive proteins and peptides are potential health-enhancing
nutraceuticals for food. Many bioactive peptides/proteins
may be used as nutraceuticals, for example, in the treatment
of cancer, asthma, diarrhea, hypertension, thrombosis, dental
diseases, as well as mineral malabsorption, and immunodeficiency.
The following components of milk are of particular interest
in the recent years: 1) Lactoferrin [Lf] has antibacterial,
antifungal, antiviral, antiparasite and antitumor activities
and accelerates immunomodulatory properties. Lf is a potent
inhibitor for several enveloped and naked viruses, such as
rotavirus, enterovirus and adenovirus. Lf is resistant to
tryptic digestion and breast-fed infants excrete high levels
of faecal Lf, so that its effect on viruses replicating in
the gastrointestinal tract is of great interest. 2) Casein
has been protective in experimental bacteremia by eliciting
myelopoiesis. Casein hydrolyzates were also protective in
diabetic animals, reduced the tumor growth and diminished
colicky symptoms in infants. 3) A Proline rich polypeptide
[PRP] revealed variety of immunotropic functions, including
promotion of T-cell activation and inhibition of autoimmune
disorders such as multiple sclerosis. 4) α-Lactalbumin
[LA] demonstrates antiviral, antitumor and anti-stress properties.
5) Lactoperoxidase shows antibacterial properties. 6) Lysozyme
is effective in treatment of periodentitis and prevention
of tooth decay. Taken together, milk-derived proteins and
peptides are bio-available and safe for the prevention and
treatment of various disorders in humans and may play a complementary
[natural agents] rather than a substitutional role to the
toxic synthetic pharmacological drugs.
[Back to top]
Linking New Paradigms in Protein Chemistry to
Reversible Membrane Protein Interactions
Øyvind Halskau, Arturo Muga and Aurora
Martínez
Amphitrophic proteins are soluble, globular proteins
that may - under certain conditions - interact reversibly
with a plasma membrane. How this apparent duality in the properties
of a protein is achieved has been a relatively little studied
subject until recently. In this review we aim to summarize
the current knowledge regarding some important amphitrophic
systems in which the interaction with the membrane does not
require post-translational functional groups, but is an intrinsic
property of the protein. We discuss mechanisms and driving
forces involved in membrane binding in the context of two
related concepts in protein folding and function that appear
to have implications for understanding the association of
proteins with membranes; first, the existence of some proteins
with low-energy barrier heights for protein folding. Low folding
barriers and the ability of proteins to form stable molten
globule states are rationales that can explain how a protein
can gain access to an ensemble (or continuum) of non-native
conformations that are competent membrane binders. Second,
the focus on order-disorder and disorder-order transitions
to explain protein function, a concept which has been mainly
developed within the novel protein trinity paradigm.
Here, protein function can arise from any of three thermodynamic
states: a solid, crystal-like state; a dense fluid state.
and an extended disordered state. Together these concepts
aid to understand amphitrophic mechanism and to unify interpretations
of protein behaviour with respect to the degree of 8 (un)folding
of the membrane-bound proteins.
[Back to top]
Metallothioneins and Cancer
Tomas Eckschlager, Vojtech Adam, Jan Hrabeta, Katarina Figova
and Rene Kizek
Metallothioneins (MTs) are low molecular, cysteine-rich
proteins that have naturally-occurring Zn2+
in both clusters. They may serve as a reservoir of metals
for synthesis of apoenzymes and zinc-finger transcription
regulators. MTs are also involved with several important proteins
e.g. p53, NF-κB,
PKCl, and GTPase Rab3A. New biological roles for these proteins
have been identified including those needed in the carcinogenic
process. However, their use as a predictive marker remains
controversial. Several reports have disclosed MTs expression
as a prognostic factor for tumor progression and drug resistance
in a variety of malignancies particularly breast, prostatic,
ovarial, head and neck, non-small cell lung cancer, melanoma,
and soft tissue sarcoma. The role of MTs as a tumor disease
marker or as a cause of resistance in cancer treatment is
reviewed and discussed. Moreover, we describe some analytical
methods that were developed to detect MTs.
[Back to top]
Quantitative Investigation of Biomolecular Interactions
in Crowded Media by Fluorescence Spectroscopy, a Good Choice
Silvia Zorrilla and M. Pilar Lillo
Fluorescence spectroscopy methods have been proved to
be powerful tools for the quantitative investigation of homologous
and heterologous interactions, rotational and translational
diffusion, and structural dynamics of biological molecules
in crowded media. In addition to their high sensitivity, these
methods present the advantage that the selective fluorescent
labeling of the biomolecules under study allows distinguishing
them from the background species. Moreover, the recent development
of biological applications of single molecule fluorescence
micro-spectroscopy methods has opened the possibility of performing
quantitative determinations inside cells. In the last decades,
theoretical and experimental studies have demonstrated the
possible influence of the high concentration of macromolecules
within living systems, on the thermodynamics and kinetics
of biological reactions. Therefore, there is a growing interest
in quantitatively evaluating the interactions involving biomolecules
in the natural environment in which they occur. Since this
is not always feasible, experiments conducted in model crowded
conditions, resembling physiological media, may contribute
to reduce the gap between traditional in vitro and
in vivo experiments. In this review we will discuss
the application of some fluorescence spectroscopy approaches,
for the identification and quantification of biological macromolecules
and their functional interactions in model crowded conditions.
[Back to top]
Diverse Roles of GADD45α
in Stress Signaling
Ming Gao, Ning Guo, Chuanshu Huang and Lun Song
Mammalian cells are prone to tumorigenesis when suffering
the genotoxic stresses, and the existence of the tumor suppressors
validly decrease this possibility. Gadd45α
is one of the growth arrest and DNA
damage-inducible (Gadd) 45 gene family members
and serves as a stress sensor and tumor suppressor under most
stress conditions, which is evidenced by cell cycle arrest,
DNA repair, senescence or apoptosis triggered by induction
of GADD45α
expression. However, some recent reports have challenged
this notion by demonstrating the correlation of GADD45α
expression to cell survival and even progression of
certain tumor cells. Therefore, GADD45α
seems to exert multiple roles in stress signaling
and tumor development. Elucidation of the related mechanisms
will be helpful for the establishment of novel tumor therapeutic
strategy targeting GADD45α.
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