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Current
Protein & Peptide Science
ISSN: 1389-2042
Current Protein and Peptide
Science
Volume 9, Number 2, April 2008
Contents
Rooteomics: The Challenge of Discovering Plant-Defense-Related
Proteins in Roots Pp. 108-116
Angela Mehta, Beatriz S. Magalhães, Djair S. L.
Souza,Erico A.R.Vasconcelos, Luciano P. Silva, Maria Fátima
Grossi-deSa, OctávioL. Franco, Paulo H.A. da Costa
and Thales L. Rocha
[Abstract]
Structure-Based Drug Design Targeting Biosynthesis
of Isoprenoids:A Crystallographic State of the Art of the
Involved Enzymes Pp. 117-137
J. de Ruyck and J. Wouters
[Abstract]
Engineering the Protein Folding Landscape
in Gram-Negative Bacteria Pp. 138-149
Thomas J. Mansell, Adam C. Fisher and Matthew P. DeLisa
[Abstract]
The Structural Analysis of Large Noncovalent Oxygen Binding
Proteins by MALLS and ESI-MS: A Review on Annelid Hexagonal
Bilayer Hemoglobin and Crustacean Hemocyanin Pp.
150-180
Matthieu Bruneaux, Morgane Rousselot, Emmanuelle
Leize, François H. Lallier and Franck Zal
[Abstract]
Molecular Dynamics Simulations of Proteins and
Peptides: From Folding to Drug Design Pp.
181-196
Giulia Morra, Massimiliano Meli and Giorgio Colombo
[Abstract]
Diversity in Structure and Function of Tethering
Complexes: Evidence for Different Mechanisms in Vesicular
Transport Regulation Pp. 197-209
D. Kümmel and U. Heinemann
[Abstract]
Abstracts
[Back to top]
Rooteomics: The Challenge of Discovering Plant-Defense-Related
Proteins in Roots
Angela Mehta, Beatriz S. Magalhães, Djair S. L.
Souza,Erico A.R.Vasconcelos, Luciano P. Silva, Maria Fátima
Grossi-de-Sa, Octávio L. Franco, Paulo H.A. da Costa
and Thales L. Rocha
In recent years, a strong emphasis has been given in deciphering
the function of genes unraveled by the completion of several
genome sequencing projects. In plants, functional genomics
has been massively used in order to search for gene products
of agronomic relevance. As far as root-path ogen interactions
are concerned, several genes are recognized to provide tolerance/resistance
against potential invaders. However, very few proteins have
been identified by using current proteomic approaches. One
of the major drawbacks for the successful analysis of root
proteomes is the inherent characteristics of this tissue,
which include low volume content and high concentration of
interfering substances such as pigments and phenolic compounds.
The proteome analysis of plant-pathogen interactions provides
important information about the global proteins expressed
in roots in response to biotic stresses. Moreover, several
pathogenic proteins superimpose the plant proteome and can
be identified and used as targets for the control of viruses,
bacteria, fungi and nematode pathogens. The present review
focuses on advances in different proteomic strategies dedicated
to the challenging analysis of plant defense proteins expressed
during bacteria-, fungi- and nematode-root interactions. Recent
developments, limitations of the current techniques, and technological
perspectives for root proteomics aiming at the identification
of resistance-related proteins are discussed.
[Back to top]
Structure-Based Drug Design Targeting Biosynthesis
of Isoprenoids:A Crystallographic State of the Art of the
Involved Enzymes
J. de Ruyck and J. Wouters
Biosynthesis of the universal terpenoid precursors, isopentenyl
diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), from
three acetyl CoA moieties through mevalonate was studied extensively
in the 1950s. For several decades, the mevalonate paradigm
reigned supreme and a mevalonate origin was attributed to
a growing number of natural products, in many cases erroneously.
Besides this biosynthetic pathway, the existence of a second
one leading to IPP and DMAPP through 1-deoxy-D-xylulose 5-phosphate
and 2C-methyl-D-erythritol 4-phosphate was discovered more
recently in plants and some eubacteria. This pathway is widely
distributed in the bacterial kingdom including major human
pathogens, such as Mycobacterium tuberculosis
or Helicobacter pylori and is also essential in the
malaria vector Plasmodium falciparum. During the
last few years, the genes, enzymes, intermediates and mechanisms
of the biosynthetic route have been elucidated by a combination
of methods including comparative genomics, enzymology, advanced
NMR technology and crystallography. The present crystallographic
review of enzymes involved in isoprenoid biosynthesis will
be useful for understanding the various catalytic mechanisms
and could potentially help for structure-based drug design.
[Back to top]
Engineering the Protein Folding Landscape
in Gram-Negative Bacteria
Thomas J. Mansell, Adam C. Fisher and Matthew P. DeLisa
Gram-negative bacteria, especially Escherichia coli,
are often the preferred hosts for recombinant protein production
because of their fast doubling times, ability to grow to high
cell density, propensity for high recombinant protein titers
and straightforward protein purification techniques. The utility
of simple bacteria in such studies continues to improve as
a result of an ever-increasing body of knowledge regarding
their native protein biogenesis machinery. From translation
on the ribosome to interaction with cytosolic accessory factors
to transport across the inner membrane into the periplasmic
space, cellular proteins interact with many different types
of cellular machinery and each interaction can have a profound
effect on the protein folding process. This review addresses
key aspects of cellular protein folding, solubility and expression
in E. coli with particular focus on the elegant biological
machinery that orchestrates the transition from nascent polypeptide
to folded, functional protein. Specifically highlighted are
a variety of different techniques to intentionally alter the
folding environment of the cell as a means to understand and
engineer intracellular protein folding and stability.
[Back to top]
The Structural Analysis of Large Noncovalent Oxygen Binding
Proteins by MALLS and ESI-MS: A Review on Annelid Hexagonal
Bilayer Hemoglobin and Crustacean Hemocyanin
Matthieu Bruneaux, Morgane Rousselot, Emmanuelle
Leize, François H. Lallier and Franck Zal
Understanding the function of macromolecular complexes is
related to a precise knowledge of their structure. These large
complexes are often fragile high molecular mass noncovalent
multimeric proteins. Classical biochemical methods for determination
of their native mass and subunit composition were used to
resolve their quaternary structure, sometimes leading to different
models. Recently, the development of mass spectrometry and
multi-angle laser light scattering (MALLS) has enabled absolute
determination of native masses and subunit masses. Electrospray
ionization mass spectrometry (ESI-MS) was used in denaturing
and native conditions to probe subunit composition and noncovalent
assemblies masses up to 2.25 MDa. In a complementary way,
MALLS provides mass and size estimation in various aqueous
solvents. ESI-MS method can also give insights into post-translational
modifications (glycosylation, disulfide bridges …).
By combining native mass and subunit composition data, structural
models can be proposed for large edifices such as annelid
extracellular hexagonal bilayer hemoglobins (HBL Hb) and crustacean
hemocyanins (Hc). Association/dissociation mechanisms, protein-protein
interactions, structural diversity among species and environmental
adaptations can also be addressed with these methods. With
their absolute mass determination, the very high precision
of spectrometry and the versatile nature of light scattering,
ESI-MS and MALLS have provided a wealth of data helping to
resolve parts of controversies for HBL-Hb models and opening
access to new fields of investigation in structural diversity
and molecular adaptation. In this review we will focus on
annelid HBL-Hb and on crustacean Hc and on the original contributions
of ESI-MS and MALLS in this field.
[Back to top]
Molecular Dynamics Simulations of Proteins and
Peptides: From Folding to Drug Design
Giulia Morra, Massimiliano Meli and Giorgio Colombo
Computer simulations of proteins, lipids and nucleic acids
at equilibrium have become essentially routine. However, the
fact remains that complete sampling of conformational space
continues to be a bottle-neck in the field. The challenge
for the future is to overcome such problems and use computational
approaches to understand recognition and spontaneous self-organization
in biomolecular systems (folding, aggregation and assembly
of complexes), processes that cannot be directly observed
experimentally. In this review, examples illustrating the
extent to which simulations can be used to understand these
phenomena in biomolecular systems will be presented along
with examples of methodological developments to increase our
physical understanding of the processes. The study cases will
cover the problems of peptide-receptor recognition and the
use of the information obtained for the design of new non-peptidic
ligands; the study of the folding mechanism of small proteins
and finally the study of the initial stages of peptide self-aggregation
[Back to top]
Diversity in Structure and Function of Tethering
Complexes: Evidence for Different Mechanisms in Vesicular
Transport Regulation
D. Kümmel and U. Heinemann
The term ‘tethering factor’ has been coined for
a heterogeneous group of proteins that all are required for
protein trafficking prior to vesicle docking and SNARE-mediated
membrane fusion. Two groups of tethering factors can be distinguished,
long coiled-coil proteins and multi-subunit complexes. To
date, eight such protein complexes have been identified in
yeast, and they are required for different trafficking steps.
Homologous complexes are found in all eukaryotic organisms,
but conservation seems to be less strict than for other components
of the trafficking machinery. In fact, for most proposed multi-subunit
tethers their ability to actually bridge two membranes remains
to be shown. Here we discuss recent progress in the structural
and functional characterization of tethering complexes and
present the emerging view that the different complexes are
quite diverse in their structure and the molecular mechanisms
underlying their function. TRAPP and the exocyst are the structurally
best characterized tethering complexes. Their comparison fails
to reveal any similarity on a structural level. Furthermore,
the interactions with regulatory Rab GTPases vary, with TRAPP
acting as a nucleotide exchange factor and the exocyst being
an effector. Considering these differences among the tethering
complexes as well as between their yeast and mammalian orthologs
which is apparent from recent studies, we suggest that tethering
complexes do not mediate a strictly conserved process in vesicular
transport but are diverse regulators acting after vesicle
budding and prior to membrane fusion.
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