Summary: Zein seed storage protein

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Wikipedia: Zein
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Zein Edit Wikipedia article

This article's lead section may not adequately summarize key points of its contents. Please consider expanding the lead to provide an accessible overview of all important aspects of the article. (March 2012)

For other uses of "Zein", see Zein (disambiguation).

Zein

Identifiers

Symbol

Zein

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Zein is a class of prolamine protein found in maize. It is usually manufactured as a powder from corn gluten meal. (Note that "corn gluten" is colloquial jargon that describes corn proteins that are nether gliadin nor glutenin. Only wheat, barley, rye and oat contain true gluten.)

[edit] Commercial uses

Zein is one of the best understood plant proteins^[1] and has a variety of industrial and food uses.^[2]^[3] Historically, it has been used in the manufacture of a wide variety of commercial products, including coatings for paper cups, soda bottle cap linings, clothing fabric,^[4] buttons, adhesives, coatings and binders. The dominant historical use of zein was in the textile fibers market where it was produced under the name "Vicara".^[2]^[5] With the development of synthetic alternatives, the use of zein in this market eventually disappeared. By using electrospinning, zein fibers have again been produced in the lab, where additional research will be performed to re-enter the fiber market.^[6]^[7] Pure zein is clear, odorless, tasteless, hard, water-insoluble, and edible, making it invaluable in processed foods and pharmaceuticals, in competition with insect shellac. It is now used as a coating for candy, nuts, fruit, pills, and other encapsulated foods and drugs. In the United States, it may be labeled as "confectioner's glaze" (which may also refer to shellac-based glazes) and used as a coating on bakery products^[8] or as "vegetable protein." It is classified as Generally Recognized as Safe (GRAS) by the U.S. Food and Drug Administration.

Zein can be further processed into resins and other bioplastic polymers, which can be extruded or rolled into a variety of plastic products.^[9]^[10] With increasing environmental concerns about synthetic coatings (such as PFOA) and the current higher prices of hydrocarbon-based petrochemicals, there is increased focus on zein as a raw material for a variety of nontoxic and renewable polymer applications, particularly in the paper industry.^[11]^[12] Other reasons for a renewed interest in zein include concern about the landfill costs of plastics, and consumer interest in natural substances. There are also a number of potential new food industry applications.

Researchers at the University of Illinois at Urbana-Champaign and at William Wrigley Jr. Company have recently been studying the possibility of using zein to replace some of the gum base in chewing gum.^[13] They are also studying medical applications such as using the zein molecule to "carry biocompounds to targeted sites in the human body".^[14] There are a number of potential food safety applications that may be possible for zein-based packaging according to several researchers. A military contractor is researching the use of zein to protect MRE food packages.^[15] Other packaging/food safety applications that have been researched include frozen foods,^[16] ready-to-eat chicken,^[17] and cheese and liquid eggs.^[18] Food researchers in Japan have noted the ability of the zein molecule to act as a water barrier.^[19]

While there are numerous existing and potential uses for zein, the main barrier to greater commercial success has been its historic high cost until recently. Some believe the solution is to extract zein as a byproduct in the manufacturing process for ethanol^[20] or in new off-shore manufacture.

[edit] Gene family

Alpha-prolamins are the major seed storage proteins of species of the grass tribe Andropogonea. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats presumed to be the result of multiple intragenic duplication.^[21] In Zea mays (Maize), the 22 kDa and 19 kDa zeins are encoded by a large multigene family and are the major seed storage proteins accounting for 70% of the total zein fraction. Structurally the 22 kDa and 19 kDa zeins are composed of nine adjacent, topologically antiparallel helices clustered within a distorted cylinder. The 22 kDa alpha-zeins are encoded by 23 genes;^[22] twenty-two of the members are found in a roughly tandem array forming a dense gene cluster. The expressed genes in the cluster are interspersed with nonexpressed genes. Interestingly, some of the expressed genes differ in their transcriptional regulation. Gene amplification appears to be in blocks of genes explaining the rapid and compact expansion of the cluster during the evolution of maize.

[edit] Other biodegradable polymers

[edit] References

^ Momany, Frank A.; Sessa, David J.; Lawton, John C.; Selling, Gordon W.; Hamaker, Sharon A. H.; and Willett, Julious L. "Structural Characterization of A-Zein" December 27, 2005, American Chemical Society
^ ^a ^b Lawton, John W. "Zein: A History of Processing and Use", November 1, 2002, American Association of Cereal Chemists
^ Gennadios, Aristippos"Protein-Based Films and Coatings" 2002
^ Commission on Life Sciences "Biobased Industrial Products: Research and Commercialization Priorities" 2002.
^ Horst, W.P. Amer Dyestuff Rep Vol. 38, 335, 1949.
^ Miyoshi, T., Toyohara, H., Minematsu, H. "Preparation of ultrafine fibrous zein membranes via electrospinning", Polymer International Vol. 54, no. 8, 2005.
^ Selling, G., Biswas, A., Patel, A., Walls, D., Dunlap, C., Wei, Y. "Impact of Solvent on Electrospinning of Zein and Analysis of Resulting Fibers", Macromolecular Chemistry and Physics Vol. 208, no. 9, 2007.
^ Kobs, Lisa "Shining Up Appearances", Food Product Design.
^ Lee, Richard "Multiple-use Corn zein-based Biodegradable Resins, Sheets, and Films are an attractive alternative to plastic", University of Illinois at Urbana-Champaign.
^ Lawton Jr., J.W. "Plasticizers for Zein:their Effect on Tensile Properties and Water Absorption of Zein Films" January 12, 2004, Cereal Chemistry.
^ Jabar, Anthony Jr; Bilodeau, Michael A.; Neivandt, David J.; Spender, Jonathan "Barrier Compositions and Articles Produced with the Compositions", December 29, 2005, United States Patent (pending)
^ Parris, Nicholas; Sykes, Marguerite; Dickey, Leland C.; Wiles, Jack L.; Urbanik, Thomas J.; Cooke, Peter H. "Recyclable zein-coated kraft paper", Progress in paper recycling Vol. 11, no. 3, May 2002.
^ McGowan B.A., Padua G.W., and Lee S-Y. "Formulation of Corn Zein Chewing Gum and Evaluation of Sensory Properties by the Time-Intensity Method", September, 2005, Journal of Food Science.
^ Picklesimer, Phyllis. "Nanotechnologist Plans to Build Things with Bricklike Corn Molecules," University of Illinois at Urbana-Champaign.
^ Bertrand, Kate, "Military packages put technology to the test," September 2005
^ Padua, Graciela W., Rakotonirainy, Andrianaivo, and Wang, Qin "Zein-Based Biodegradable Packaging for Frozen Foods", University of Illinois at Urbana-Champaign
^ Janes M.E.; Kooshesh S.; Johnson M.G. "Control of Listeria monocytogenes on the Surface of Refrigerated, Ready-to-eat Chicken Coated with Edible Zein Film" September, 2002, Journal of Food Science.
^ Dawson, Paul "Packaging Films Fight Bacteria and Help the Environment" Clemson University
^ Qiangxian Wu, Hiroshi Sakabe and Seiichiro Isobe "Studies on the toughness and water resistance of zein-based polymers by modification" June, 2003, National Food Research Institute, Japan.
^ Core, Jim. "Corn Protein Could Reduce Ethanol Production Costs," April 15, 2002, United States Department of Agriculture Agricultural Research Service.
^ Garratt R, Oliva G, Caracelli I, Leite A, Arruda P (January 1993). "Studies of the zein-like alpha-prolamins based on an analysis of amino acid sequences: implications for their evolution and three-dimensional structure". Proteins 15 (1): 88â99. doi:10.1002/prot.340150111. PMID 8451243.
^ Song R, Llaca V, Linton E, Messing J (November 2001). "Sequence, regulation, and evolution of the maize 22-kD alpha zein gene family". Genome Res. 11 (11): 1817â25. doi:10.1101/gr.197301. PMC 311139. PMID 11691845.

[edit] External links

Oregon State University Food Resource: Zein
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This article incorporates text from the public domain Pfam and InterPro IPR002530

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Zein seed storage protein Provide feedback

Zeins are seed storage proteins. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats [1].

Literature references

Garratt R, Oliva G, Caracelli I, Leite A, Arruda P; , Proteins 1993;15:88-99.: Studies of the zein-like alpha-prolamins based on an analysis of amino acid sequences: implications for their evolution and three-dimensional structure. PUBMED:8451243 EPMC:8451243

External database links

PANDIT:	PF01559
Pseudofam:	PF01559
SYSTERS:	Zein

This tab holds annotation information from the InterPro database.

InterPro entry IPR002530

Alpha-prolamins are the major seed storage proteins of species of the grass tribe Andropogonea. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats presumed to be the result of multiple intragenic duplication [PUBMED:8451243]. In Zea mays (Maize), the 22 kDa and 19 kDa zeins are encoded by a large multigene family and are the major seed storage proteins accounting for 70% of the total zein fraction. Structurally the 22 kDa and 19 kDa zeins are composed of nine adjacent, topologically antiparallel helices clustered within a distorted cylinder. The 22 kDa alpha-zeins are encoded by 23 genes [PUBMED:11691845]; twenty-two of the members are found in a roughly tandem array forming a dense gene cluster. The expressed genes in the cluster are interspersed with nonexpressed genes. Interestingly, some of the expressed genes differ in their transcriptional regulation. Gene amplification appears to be in blocks of genes explaining the rapid and compact expansion of the cluster during the evolution of maize.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

nutrient reservoir activity (GO:0045735)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (9)	Full (325)	Representative proteomes				NCBI (337)	Meta (0)
	Seed (9)	Full (325)	RP15 (0)	RP35 (22)	RP55 (22)	RP75 (22)	NCBI (337)	Meta (0)
Jalview	View	View		View	View	View	View
HTML	View	View		View	View	View
PP/heatmap	₁	View		View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (9)	Full (325)	Representative proteomes				NCBI (337)	Meta (0)
	Seed (9)	Full (325)	RP15 (0)	RP35 (22)	RP55 (22)	RP75 (22)	NCBI (337)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (9)	Full (325)	Representative proteomes				NCBI (337)	Meta (0)
	Seed (9)	Full (325)	RP15 (0)	RP35 (22)	RP55 (22)	RP75 (22)	NCBI (337)	Meta (0)
Raw Stockholm	Download	Download		Download	Download	Download	Download
Gzipped	Download	Download		Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_181 (release 4.0)

Previous IDs:

none

Type:

Family

Author:

Bateman A

Number in seed:

9

Number in full:

325

Average length of the domain:

134.90 aa

Average identity of full alignment:

41 %

Average coverage of the sequence by the domain:

97.79 %

HMM information

HMM build commands:

build method: hmmbuild --amino -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	24.6	24.6
Trusted cut-off	26.1	24.6
Noise cut-off	21.3	23.8

Model length:

246

Family (HMM) version:

11

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Zein (PF01559)

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