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FAQ's
Q.1
What is ProGlycProt?
Ans.
ProGlycProt is a manually curated, exclusive repository of comprehensive information on experimentally characterized glycoproteins that belong to eubacteria and archaea For the benefit of users, ProGlycProt database (ProGlycProtdb) is arranged in following two sections:
1)
ProCGP (Prokaryotic Characterized Glycoproteins) defined as a compilation of prokaryotic glycoproteins for which at least one glycosite i.e. the glycosylated residue is identified through experiments like edman degradation, mass spectroscopy, site directed mutagenesis etc.
2)
ProUGP (Prokaryotic Uncharacterized Glycoproteins) defined as a list of prokaryotic glycoproteins in which glycosylation is known by experiments like aberrant migration on SDS PAGE, lectin binding, sugar specific staining but not the glycosites.
In addition, ProGlycProt provides for separate structure gallery, relevant links and two new tools that are developed keeping in mind the new sequon information obtained from literature on prokaryotic glycoproteins.
 
Q.2
What is the rationale and vision behind creation of ProGlycProt?
Ans.
Once thought restricted to eukaryotes, glycoproteins are now known to exist in almost all major phyla of prokaryotes. In last ten years, many new prokaryotic glycoproteins have been characterized for the precise location of glycosites, indicating a rising interest in the biology of protein glycosylation in prokaryotes. However, according to our search, currently none of the available protein informatic or glycoinformatic resource provides comprehensive and exclusive information about these experimentally identified or characterized glycoproteins of archaea and eubacteria. ProGlycProt is therefore designed to fill in this void. A long-term vision of ProGlycProt is to provide as much as possible experimental information available in published literature about these glycoproteins and to link these with the experimental information on mechanisms and genetic machinery involved in glycosylation of these proteins.
 
Q.3
What is different or unique in ProGlycProtdb?
Ans.
To the best of our knowledge, ProGlycProtdb is the first manually curated, exclusive database of experimentally detected/characterized glycoproteins of prokaryotic origin. Though parts of the data available at ProGlycProt can be retrieved at SwissProt/ PDB/ BCSDB/ O- GlycBase yet unlike all these repositories ProGlycProt is an exclusive compilation of experimentally validated glycoproteins of prokaryotes only. Furthermore, ProGlycProtdb provides a lot of additional interesting information about a given glycoprotein like; full structure of attached glycan (IUPAC linear notation) as available from literature, information about glycosylation linked genes, experimental methods used to characterize a given glycoprotein, year of detection, year of characterization, observed sequon features and mannual annotation of all characterized glycoprotein sequences to incorporate mutational changes/ sequence conflicts/ in vitro or in vivo engineered sequence and visual display of glycosites. This first release of ProGlycProt contains information about at least 108 experimentally known glycoproteins that are absent in SwissProt on account of unsequenced genomes of the related organisms and as many as 69 proteins that includes peptides & engineered proteins for which glycosites are yet not annotated in any of the above mentioned protein databases.
 
Q.4
Does ProGlycProtdb represent all known prokaryotic glycoproteins?
Ans.
As of now and to the best of our knowledge, ProGlycProtdb represents the largest compilation of characterized prokaryotic glycoproteins available online consisting of entries from year 1974 to June 2011. Though we may not claim that ProCGP is a complete compilation, yet we have taken best efforts to incorporate all data that we could search through literature until we stopped finding further references in our searches made until June 30, 2011, in this first release. Further, we have tried to provide as accurate as possible information, yet we encourage users to refer the original literature cited along.
On the other hand, ProUGP is compiled from various brief seed compilations available in some of the published reviews (included in bibliography) and a few selected research publications. In view of increasing availability of huge data on detection of new glycoproteins using high throughput techniques like mass spectroscopy, we believe ProUGP would be enriched exponentially in future updates. We shall derive a different scheme to accommodate all such entries under ProUGP in future updates. In current release, what we have ensured is that at least all previously compiled prokaryotic glycoproteins are made available at ProUGP; at one place; in fully cross-referenced and searchable format, with additional information.
 
Q.5
What is the Scope of ProGlycProt?
Ans.
In the last one decade, a lot of interest is generated in studying glycoproteins and mechanisms of their glycosylation in bacteria and archaea. In the first release, we have tried to provide all around information about a number of glycoproteins that are implicated in virulence, host pathogen interactions, immune modulation, disease diagnosis, and vaccination that microbiologists, clinicians, immunologists or even glycobiologists may find interesting. Similarly, we have included at least 7 glycoengineered proteins/ peptides of prokaryotic origin with known glycosites in ProCGP that may find attention of protein engineers. Further, data on glycosites can be of use for statistical analysis of sequence requirements/ preferences for glycosylation in prokaryotes
 
Q.6
Future Plans for ProGlycProt?
Ans.
Apart from continued compilations for bacterial and archaeal glycoproteins; in future updates, we aim at incorporating some or all of the following features in ProGlycProt:
¤
More structural and image inputs for glycan entries corresponding to each glycoprotein entry in ProCGP
¤
More experimental information about prokaryotic Oligosaccharyl Transferases (OSTs) and associated Glycosyl Transferases (GTs)
¤
To devise finer criteria to arrange large amount of glycoprotein entries detected by high throughput analysis like mass spectroscopy etc. under ProUGP and to facilitate better retrieval of biologically relevant and experiments oriented information about each entry.
¤
New tool(s) for glycoprotein/ sequence analysis or visualization
   
 
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Glossary of Terms used in ProGlycProtdb
S. No.
Term/Acronym
Definition
1.
AAL
Aleuria Aurantia Lectin
2.
ABEE
p-Aminobenzoic acid ethyl ester
3.
Amino sugar
Monosaccharide with one hydroxyl group (-OH) replaced by an amine group (-NH2).
4.
Bac
Bacillosamine (2, 4-diacetamido-2, 4, 6-trideoxyglucopyranose).
5.
CAD/CID
Collision-Activated (or –induced) Dissociation
6.
CapLC-MS/MS
Capillary Liquid Chromatography-Tandem Mass Spectrometry
7.
S (Cys) linked glycosylation
Refers to the covalent linkage between glycan and sulphur atom of cysteine residue in a protein sequence
8.
COSY
Correlated Spectroscopy
9.
DATDH
2,4-Di-Acetamido-2,4,6-Tri -DeoxyHexose
10.
Deglycosylation
Removal of glycans from the glycoproteins by chemical or enzymatic methods.
11.
DIG Glycan detection
Method of detection of Digoxigenin (DIG)-labeled glycoconjugates using enzyme immunoassay
12.
Dolichol
An isoprenoid lipid with 15-19 isoprenoid units and a terminal phosphorylated hydroxyl group. Dolichol acts as a membrane bound carrier for sugars in the synthesis of glycoprotens and glycolipids
13.
DQF-COSY
Double Quantum Filtered Correlation Spectroscopy
14.
ECD
Electron Capture Dissociation
15.
Endo Hf
Endoglycosidase H leaves one GlcNAc residue attached to Asn by cleaving between the two GlcNAc residues of the N-glycan core.
16.
Engineered glycoprotein
A protein naturally unglycosylated or a synthetic peptide that is glycosylated in vitro or in vivo by chemical or enzymatic methods (usually after mutation of one or a few residues). Such proteins are also termed as neoglycoproteins.
17.
ESI Q-TOF-MS
Electrospray Ionization Quadrupole Time Of Flight Mass Spectrometry
18.
ETD
Electron Transfer Dissociation
19.
FAB-MS
Fast Atom Bombardment-Mass Spectrometry
20.
FT-ICR-MS
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
21.
Fuc
Fucose
22.
FucNAc
N-Acetylfucosamine
23.
GAGs
Glycosaminoglycans
24.
Gal
Galactose
25.
GalNAc
N-Acetyl-D-Galactosamine
26.
GATDH
2-Acetamido 4-Glyceramido 2,4,6-Trideoxyhexose Or 2- Glyceramido 4- Acetamido 2,4,6-Trideoxyhexose
27.
GC
Gas Chromatography
28.
GC-MS
Gas Chromatography-Mass Spectrometry
29.
Glc
Glucose
30.
GlcA
Glucuronic acid
31.
GlcNAc
N-Acetyl-D-Glucosamine (NAG)
32.
Glycoform
One of the differentially glycosylated forms of a glycoprotein. Glycoforms of a glycoprotein have the same protein sequence but differ in the number and/or structure of oligosaccharides attached

33.

Glycoprotein
Protein with one or more covalently bound glycans added as a co-translational or post-translational modification. The glycan may be a monosaccharide, an oligosaccharide or a polysaccharide.
34.
Glycosidase
Enzyme catalyzing the hydrolysis of a glycosidic linkage
35.
Glycosidic linkage (bond)
The bond linking monosaccharides in didiasaccharides and polysaccharides. Formed by a condensation reaction between teo OH groups, one from each of the two monosaccharides.
36.
Glycosite
An amino acid residue where glycosylation occurs in a protein sequence.
37.
Glycosyltransferase (GT)
Enzyme (with EC 2.4.X.X) catalyzing the transfer of a sugar from a nucleotide (nucleoside phosphate) sugar donor to
an acceptor substrate to form a glycosidic linkage
38.
HMBC
Heteronuclear Multiple Bond Coherence
39.
HMQC
Heteronuclear Multiple Quantum Correlation
40.
HPAEC
High-Performance Anion-Exchange Chromatography
41.
HPLC
High Pressure Liquid Chromatography
42.
HSQC
Heteronuclear Single Quantum Coherence
43.
IdoA
Iduronic Acid
44.
Lectin
A glycan binding protein with a carbohydrate-recognition domain (CRD) homologous to the sugar binding region of leguminous plant lectin.
45.
LFA
Limax Flavus Agglutinin (Sialic acid-specific lectin)
46.
MALDI-TOF MS
Matrix Assisted Laser Desorption/Ionization Time Of Flight Mass Spectrometry
47.
Man
Mannose
48.
MS-MS
Tandem Mass Spectrometry
49.
Nano-LC-MS/MS
Nano Liquid Chromatography-Tandem Mass Spectrometry
50.
nESI-feCID-MS/MS
Nano-Electrospray Ionization–Front-End Collision-Induced Dissociation Tandem Mass Spectrometry
51.
NeuNAc (NANA)
N-Acetyl Neuraminic Acid (Sialic acid)
52.
N (Asn) linked glycosylation
Refers to the covalent linkage between glycan and amide nitrogen of an aspargine residue in a protein sequence
53.
NMR
Nuclear Magnetic Resonance
54.
NOESY
Nuclear Overhauser Effect Spectroscopy
55.
O (Ser/ Thr/ Tyr) linked glycosylation
Refers to the covalent linkage between glycan and oxygen of hydroxyl group of serine/ threonine or tyrosine in a protein sequence
56.
OST
Oligo Saccharyl Transferase, the enzyme responsible for catalyzing the transfer of a precursor glycan from a sugar carrier to the protein or peptide
57.
PAS staining
Periodic Acid-Schiff staining
58.
PNGase F
Peptide N-glycosidase F that cleaves between the innermost GlcNAc and the Asn residue of an N linked oligosaccharide.
59.
Pro-Q Emerald glycostaining
A derivative of dansyl hydrazide that provides for fluorescent staining of glycoproteins
60.
PTM
Post Translational Modification
61.
Reducing end (of the glycan)
The free end of a disaccharide, polysaccharide or oligosaccharide (glycan) that retains the carbonyl function and can act as a reducing agent. In glycoproteins, it is the end of the glycan attached to the protein or peptide.
62.
RP-HPLC
Reversed Phase High Pressure Liquid Chromatography
63.
SBA
SoyBean Agglutinin (lectin)
64.
Sequon
Sequence of conserved amino acids around residue that gets glycosylated
65.
STT3
Staurosporine- and Temperature-Sensitive mutant 3, the catalytic subunit of eukaryotic multisubunit oligosaccharyl transferase
66.
TFA
Tri Fluoro Acetic Acid
67.
TFMS
Tri Fluoro Methane Sulfonic Acid
68.
TOCSY
Total Correlation Spectroscopy
69.
Xyl
Xylose
70.
ß-elimination
Base-catalyzed nonhydrolytic cleavage of glycosidic bonds between O-linked glycans and the ß-hydroxyl groups of serine or threonine residues of a protein or peptide.
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