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1.
A dynamic view of peptides and proteins in membranes 总被引:1,自引:0,他引:1
Bechinger B 《Cellular and molecular life sciences : CMLS》2008,65(19):3028-3039
Biological membranes are highly dynamic supramolecular arrangements of lipids and proteins, which fulfill key cellular functions.
Relatively few high-resolution membrane protein structures are known to date, although during recent years the structural
databases have expanded at an accelerated pace. In some instances the structures of reaction intermediates provide a stroboscopic
view on the conformational changes involved in protein function. Other biophysical approaches add dynamic aspects and allow
one to investigate the interactions with the lipid bilayers. Membrane-active peptides fulfill many important functions in
nature as they act as antimicrobials, channels, transporters or hormones, and their studies have much increased our understanding
of polypeptide-membrane interactions. Interestingly several proteins have been identified that interact with the membrane
as loose arrays of domains. Such conformations easily escape classical high-resolution structural analysis and the lessons
learned from peptides may therefore be instructive for our understanding of the functioning of such membrane proteins.
Received 11 March 2008; received after revision 2 May 2008; accepted 5 May 2008 相似文献
2.
Zinc binding to peptide analogs of the structural zinc site in alcohol dehydrogenase: Implications for an entatic state 总被引:1,自引:0,他引:1
Bergman T Zhang K Palmberg C Jörnvall H Auld DS 《Cellular and molecular life sciences : CMLS》2008,65(24):4019-4027
Zinc binding to the peptide replica and analogs to residues 93–115 of horse liver alcohol dehydrogenase (ADH) was examined
by competition of the peptides and the chromophoric chelator 4-(2- pyridylazo)resorcinol for zinc and X-ray absorption fine
structure analysis of the zinc ligands. In the enzyme, zinc is coordinated by four Cys residues. In the peptide replica, zinc
is bound to three Cys and one His residue. A four-Cys zinc coordination is observed only when His is removed, leading to increased
zinc stability. ADH crystal structures reveal that the ε-amino group of the conserved residue Lys323 is within H-bond distance
of the backbone amide oxygens of residues 103, 105 and 108, likely stabilizing the zinc coordination in the enzyme. The peptide
data thus indicate structural strain and increased energy in the zinc-binding site in the protein, characteristic of an entatic
state, implying a functional nature for this zinc site.
Received 3 July 2008; received after revision 11 August 2008; accepted 1 September 2008 相似文献
3.
4.
The elucidation of assembly pathways of multi-subunit membrane proteins is of growing interest in structural biology. In this
study, we provide an analysis of the assembly of the asymmetrically oriented PsaC subunit on the pseudo C2-symmetric Photosystem I core. Based on a comparison of the differences in the NMR solution structure of unbound PsaC with
that of the X-ray crystal structure of bound PsaC, and on a detailed analysis of the PsaC binding site surrounding the FX iron-sulfur cluster, two models can be envisioned for what are likely the last steps in the assembly of Photosystem I. Here,
we dissect both models and attempt to address heretofore unrecognized issues by proposing a mechanism that includes a thermodynamic
perspective. Experimental strategies to verify the models are proposed. In closing, the evolutionary aspects of the assembly
process will be considered, with special reference to the structural arrangement of the PsaC binding surface.
Received 22 October 2008; received after revision 17 November 2008; accepted 05 December 2008 相似文献
5.
Dynamic protein methylation in chromatin biology 总被引:1,自引:1,他引:0
6.
Mass spectrometry for protein and peptide characterisation 总被引:5,自引:0,他引:5
Jonsson AP 《Cellular and molecular life sciences : CMLS》2001,58(7):868-884
Mass spectrometry has become an important analytical tool in biological and biochemical research. Its speed, accuracy and
sensitivity are unmatched by conventional analytical techniques. Identification of proteins and characterisation of their
primary structure is a rapidly growing field in the post-genomic era, where matrix-assisted laser desorption/ionisation time-of-flight
peptide mass fingerprinting combined with electrospray tandem mass spectrometry can efficiently solve many questions. Many
recently determined genomic sequences have not been characterised at the protein level. Analysis of the amino acid sequence
and characterisation of post-translational modifications are therefore important steps towards correlation of protein structure
with function. This review concerns methods, instrumentation and applications of mass spectrometry in protein and peptide
analysis.
Received 17 April 2001; accepted 19 April 2001 相似文献
7.
The cell-cell adhesion molecule E-cadherin 总被引:11,自引:0,他引:11
8.
B. Schäfer C. Götz J. Dudek A. Hessenauer U. Matti M. Montenarh 《Cellular and molecular life sciences : CMLS》2009,66(2):339-349
Protein kinase CK2 is a highly conserved serine/threonine kinase that is ubiquitously expressed in eukaryotic cells. CK2 is
a constitutively active tetrameric enzyme composed of two catalytic α and/or α’-subunits and two regulatory β-subunits. There
is increasing evidence that the individual subunits may have independent functions and that they are asymmetrically distributed
inside the cell. To gain a better understanding of the functions of the individual subunits, we employed a yeast-two-hybrid
screen with CK2α and CK2α’. We identified the motor neuron protein KIF5C as a new binding partner for CK2. The interaction
found in the yeast-two-hybrid screen was confirmed by co-sedimentation analysis on a sucrose density gradient and by co-immunoprecipitation
analysis. Pull-down experiments and surface plasmon resonance spectrometry revealed a direct binding of KIF5C to CK2α’. Co-localization
studies with neuroblastoma cells, bone marrow and with primary neurons confirmed the biochemical analysis that KIF5C preferentially
bound to CK2α’.
Received 8 August 2008; received after revision 3 November 2008; accepted 4 November 2008 相似文献
9.
Gemoll T Habermann JK Lahmann J Szymczak S Lundgren C Bündgen NK Jungbluth T Nordström B Becker S Lomnytska MI Bruch HP Ziegler A Hellman U Auer G Roblick UJ Jörnvall H 《Cellular and molecular life sciences : CMLS》2012,69(2):325-333
DNA aneuploidy has been identified as a prognostic factor in the majority of epithelial malignancies. We aimed at identifying ploidy-associated protein expression in endometrial cancer of different prognostic subgroups. Comparison of gel electrophoresis-based protein expression patterns between normal endometrium (n?=?5), diploid (n?=?7), and aneuploid (n?=?7) endometrial carcinoma detected 121 ploidy-associated protein forms, 42 differentially expressed between normal endometrium and diploid endometrioid carcinomas, 37 between diploid and aneuploid endometrioid carcinomas, and 41 between diploid endometrioid and aneuploid uterine papillary serous cancer. Proteins were identified by mass spectrometry and evaluated by Ingenuity Pathway Analysis. Targets were confirmed by liquid chromatography/mass spectrometry. Mass spectrometry identified 41 distinct polypeptides and pathway analysis resulted in high-ranked networks with vimentin and Nf-κB as central nodes. These results identify ploidy-associated protein expression differences that overrule histopathology-associated expression differences and emphasize particular protein networks in genomic stability of endometrial cancer. 相似文献
10.
Engen JR Wales TE Hochrein JM Meyn MA Banu Ozkan S Bahar I Smithgall TE 《Cellular and molecular life sciences : CMLS》2008,65(19):3058-3073
Src-family kinases are modular signaling proteins involved in a diverse array of cellular processes. All members of the Src
family share the same domain organization, with modular SH3, SH2 and kinase domains followed by a C-terminal negative regulatory
tail. X-ray crystallographic analyses of several Src family members have revealed critical roles for the SH3 and SH2 domains
in the down-regulation of the kinase domain. This review focuses on biological, biophysical, and computational studies that
reveal conformationally distinct active states within this unique kinase family.
Received 10 March 2008; received after revision 17 May 2008; accepted 21 May 2008 相似文献
11.
Jensen MR Hass MA Hansen DF Led JJ 《Cellular and molecular life sciences : CMLS》2007,64(9):1085-1104
Metal ions play a key role for the function of many proteins. The interaction of the metal ion with the protein and its involvement
in the function of the protein vary widely. In some proteins, the metal ion is bound tightly to the ligand residues and may
be the key player in the function of the protein, as in the case of blue copper proteins. In other proteins, the metal ion
is bound only temporarily and loosely to the protein, as in the case of some metalloenzymes and other proteins where the metal
ion acts as a cofactor necessary for the function of the protein. Such proteins are often known as metal ion-activated proteins.
The review focuses on recent nuclear magnetic resonance (NMR) studies of a series of metal-dependent proteins and the characterization
of the metal-binding sites. In particular, we focus on NMR techniques for studying metal binding to proteins such as chemical
shift mapping, paramagnetic NMR and changes in backbone dynamics upon metal binding.
Received 12 October 2006; received after revision 30 November 2006; accepted 5 February 2007 相似文献
12.
Mitochondrial dysfunction and protein kinase C (PKC) activation are consistently found in diabetic cardiomyopathy but their
relationship remains unclear. This study identified mitochondrial aconitase as a downstream target of PKC activation using
immunoblotting and mass spectrometry, and then characterized phosphorylation-induced changes in its activity in hearts from
type 1 diabetic rats. PKCβ2 co-immunoprecipitated with phosphorylated aconitase from mitochondria isolated from diabetic hearts. Augmented phosphorylation
of mitochondrial aconitase in diabetic hearts was found to be associated with an increase in its reverse activity (isocitrate
to aconitate), while the rate of the forward activity was unchanged. Similar results were obtained on phosphorylation of mitochondrial
aconitase by PKCβ2 in vitro. These results demonstrate the regulation of mitochondrial aconitase activity by PKC-dependent phosphorylation. This may
influence the activity of the tricarboxylic acid cycle, and contribute to impaired mitochondrial function and energy metabolism
in diabetic hearts.
Received 31 October 2008; received after revision 17 December 2008; accepted 2 January 2009 相似文献
13.
Symmetric DNA sequence motifs allow the formation of palindromic protein/DNA complexes. Although symmetric protein sequence
motifs are less common, recent structural discoveries have unraveled a few protein/protein complexes with palindromic symmetry.
Remarkably, symmetric protein/protein complexes can be generated either by adjacent or remote sequence motifs, which may be
repeated or inverted. This contribution reflects and comments on recent findings of palindromic protein/protein complexes.
Received 14 May 2008; received after revision 21 June 2008; accepted 14 July 2008 相似文献
14.
Porcelli AM Ghelli A Iommarini L Mariani E Hoque M Zanna C Gasparre G Rugolo M 《Cellular and molecular life sciences : CMLS》2008,65(18):2943-2951
Human thyroid carcinoma XTC.UC1 cells harbor a homoplasmic frameshift mutation in the MT-ND1 subunit of respiratory complex
I. When forced to use exclusively oxidative phosphorylation for energy production by inhibiting glycolysis, these cells triggered
a caspase-independent cell death pathway, which was associated to a significant imbalance in glutathione homeostasis and a
cleavage of the actin cytoskeleton. Overexpression of the anti-apoptotic Bcl-2 protein significantly increased the level of
endogenous reduced glutathione, thus preventing its oxidation after the metabolic stress. Furthermore, Bcl-2 completely inhibited
actin cleavage and increased cell adhesion, but was unable to improve cellular viability. Similar effects were obtained when
XTC.UC1 cells were incubated with exogenous glutathione. We hence propose that Bcl-2 can safeguard cytoskeletal stability
through an antioxidant function.
Received 28 May 2008; received after revision 8 July 2008; accepted 29 July 2008 相似文献
15.
Antisense transcription: A critical look in both directions 总被引:3,自引:1,他引:2
16.
Proliferating cell nuclear antigen: a proteomics view 总被引:3,自引:0,他引:3
Naryzhny SN 《Cellular and molecular life sciences : CMLS》2008,65(23):3789-3808
Proliferating cell nuclear antigen (PCNA), a cell cycle marker protein, is well known as a DNA sliding clamp for DNA polymerase
delta and as an essential component for eukaryotic chromosomal DNA replication and repair. Due to its mobility inside nuclei,
PCNA is dynamically presented in a soluble or chromatin-associated form. The heterogeneity and specific modifications of PCNA
may reflect its multiple functions and the presence of many binding partners in the cell. The recent proteomics approaches
applied to characterizing PCNA interactions revealed multiple PCNA partners with a wide spectrum of activity and unveiled
the possible existence of new PCNA functions. Since more than 100 PCNA-interacting proteins and several PCNA modifications
have already been reported, a proteomics point of view seems exactly suitable to better understand the role of PCNA in cellular
functions.
Received 29 May 2008; received after revision 7 July 2008; accepted 16 July 2008 相似文献
17.
Lage H 《Cellular and molecular life sciences : CMLS》2008,65(20):3145-3167
Although various mechanisms involved in anticancer multidrug resistance (MDR) can be identified, it remains a major problem
in oncology. Beyond that, the introduction of new “targeted” drugs have not solved the problem. On the contrary, it has been
demonstrated that the “classical” MDR-associated mechanisms are similar or identical to those causing resistance to these
novel agents. These mechanisms include the enhanced activity of drug pumps, i.e. ABC or alternative transporters; modulation
of cellular death pathways; alteration and repair of target molecules; and various less common mechanisms. Together they build
a complex network of cellular pathways and molecular mechanisms mediating an individual MDR phenotype. Although the application
of new high throughput “-omics” technologies have identified multiple new gene-/protein expression signatures or factors associated
with drug resistance, so far none of these findings has been useful for creating improved diagnostic assays, for prediction
of individual therapy response, or for development of updated chemosensitizers.
Received 05 March 2008; received after revision 21 May 2008; accepted 23 May 2008 相似文献
18.
Eukaryotic genomes have complex spatial organization in the nucleus. The factors and the mechanisms involved in this organization
remain an enigma. Among the many proteins implicated in such a role, the ubiquitous Zn-finger protein CTCF stands out. Here
we summarize the evidence placing CTCF in the enviable position of a master organizer of the genome. CTCF can form loops in cis, and can bridge sequences located on different chromosomes in trans. The thousands of CTCF binding sites, identified in recent genome-wide localization studies, and their distribution along
the genome further support a crucial role of CTCF as a chromatin organizer.
Received 10 October 2008; received after revision 11 December 2008; accepted 16 December 2008 相似文献
19.
A. Simonetti S. Marzi L. Jenner A. Myasnikov P. Romby G. Yusupova B. P. Klaholz M. Yusupov 《Cellular and molecular life sciences : CMLS》2009,66(3):423-436
The assembly of the protein synthesis machinery occurs during translation initiation. In bacteria, this process involves the
binding of messenger RNA(mRNA) start site and fMet-tRNAfMet to the ribosome, which results in the formation of the first codon-anticodon interaction and sets the reading frame for the
decoding of the mRNA. This interaction takes place in the peptidyl site of the 30S ribosomal subunit and is controlled by
the initiation factors IF1, IF2 and IF3 to form the 30S initiation complex. The binding of the 50S subunit and the ejection
of the IFs mark the irreversible transition to the elongation phase. Visualization of these ligands on the ribosome has been
achieved by cryo-electron microscopy and X-ray crystallography studies, which has helped to understand the mechanism of translation
initiation at the molecular level. Conformational changes associated with different functional states provide a dynamic view
of the initiation process and of its regulation.
Received 16 July 2008; received after revision 31 August 2008; accepted 10 September 2008
A. Simonetti, S. Marzid: These authors contributed equally to this work. 相似文献
20.
F. Magherini A. Carpentieri A. Amoresano T. Gamberi C. De Filippo L. Rizzetto M. Biagini P. Pucci A. Modesti 《Cellular and molecular life sciences : CMLS》2009,66(5):933-947
In this study, a proteomic approach that combines selective labelling of proteins containing reduced cysteine residues with
two-dimensional electrophoresis/mass spectrometry was used to evaluate the redox state of protein cysteines during chronological
ageing in Saccharomyces cerevisiae. The procedure was developed on the grounds that biotinconjugated iodoacetamide (BIAM) specifically reacts with reduced cysteine
residues. BIAM-labelled proteins can then be selectively isolated by streptavidin affinity capture. We compared cells grown
on 2% glucose in the exponential phase and during chronological ageing and we found that many proteins undergo cysteine oxidation.
The target proteins include enzymes involved in glucose metabolism. Both caloric restriction and growth on glycerol resulted
in a decrease in the oxidative modification. Furthermore, in these conditions a reduced production of ROS and a more negative
glutathione half cell redox potential were observed.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Received 15 September 2008; received after revision 17 December 2008; accepted 06 January 2009 相似文献