Protein Domain

How do I know which part of a protein is in the extracellular domain?
I know that the extracellular domain is the part that sticks out of the membrane but the resources I have found do not go into anymore detail. Please help me find something that expains it better.

The easiest way I know is that that portion which is in the extracellular domain would have to be hydrophillic (water loving) the hydrophobic (water fearing) portions want to reside inside the plasma membrane (cell membrane) as the inside of the plasma membrane are also hydrophobic. THis also mean though that something that is hydrophilic also will be happy in the cytoplasm side of the plasma membrane. I do not know if there is a easy way to differentiate between the protiens that hang out in the extracellular domain and the cytoplasm (cytosol).

what is protein domain?


The primary structure (string of amino acids) of a protein encodes its uniquely folded 3D conformation (Anfinsen et al., 1961 Anfinsen's Dogma). The most important factor governing the folding of a protein into 3D structure is the distribution of polar and non-polar side chains (Cordes et al., 1996). Folding is driven by the burial of hydrophobic side chains into the interior of the molecule so to avoid contact with the aqueous environment. Generally proteins have a core of hydrophobic residues surrounded by a shell of hydrophilic residues. Since the peptide bonds themselves are polar they are neutralised by hydrogen bonding with each other when in the hydrophobic environment. This gives rise to regions of the polypeptide that form regular 3D structural patterns called 'secondary structure'. There are two main types of secondary structure: α-helical β-sheet

about the protein kinase domain classification?
IN HUMAN PROTEIN KINASE IS THERE. IT ALSO HAVE DOMAINS IN IT. I WANT THE CLASSIFICATION OF THAT DOMAINS. there are 6 families in protein kinase. they have different domains in it. some of these may(may not )have same domain. how do find these domains. i.e for example AGC is one FAMILY of the protein kinase. it has PDB domain, STE is also one of the FAMILY of protein kinase which also have PDB domain. "my question was which tool or database can i use to find the same domains among these 6 families of protein kinase".

Not sure I understand the question. Human protein kinases (proteine kinase A, C, G, etc.) do have domains, but I'm not sure what else you want to know.

write an essay on biological functions of cytokines,discuss biologically.write an essay on protein domain.?
cytokines are soluble mediators that act as activators on certain phagocytic cells like Blymphocytes,Macrophages etc during specific immune responses.

I ain't writin' no essay!! But the topic is interesting. If you can get your hands on a Merck Manual, there's a wonderfully detailed summary of cytokines in the beginning section on Immunology. The topic of protein domains as it related to immunoglobulins is also interesting and well covered in Merck's. But what I find most interesting is the function of the thymus.

What holds protein domains together?
What types of interactions allow for protein domains to come together besides disulfide bonds?

A domain on a protein is a compactly folded region in its tertiary structure. Domains tend to be roughly 50 to 300 amino acids in length and are made by folding alpha helices, beta sheets, or a combination of the two together to form a globular unit. This folding allows the formation of multiple hydrogen bonds, which serve to stabilize the protein's structure. Also hydrophobic bonds and ionic bonds.

What is the difference between a subunit and domain in proteins?


So some proteins are made up of multiple different proteins called subunits. For example the protein hemoglobin is made of 4 different subunits...two alpha and two beta chains. All four subunits...each it's own seperate ammino acid chain make up the one protein. Domains are regions in the ammino acid chain that have a specific purpose. A single ammino acid chain can have multiple domains. Get it? It's a little confusing...but just remember a subunit is one ammino acid chain whereas a domain is just a region on the ammino acid chain. Shoot me an email if this is to confusing...might be able to dig up a picture or something.

What domain is viruses classified under?
Viruses are not derived from preexisting cells, and thus oppose the Cell Theory, and are not cells; they are simply a cluster of protein and genetic material. An organism is defined as "consisting of monomeric units known as cells". If viruses are not made up of one or more cells, they obviously cannot be considered as an organism, if they are not organisms, how can they share the same system of classification as all other organisms on Earth (specifically speaking: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)? There is also a dispute going over whether viruses are alive or not (since they cannot metabolize and reproduce independently). I have browsed through many sites on any hint on which Domain viruses are classified under, but all they tell me is the families and genus of some viruses. Which Domain do viruses belong to?

A good question, A short answer is- Viruses do not fall under any domain. They are neither prokaryotes nor eukaryotes. They are not considered a part of the classical living world. Therefore, their system of classification is entirely different. Here is my answer in detail: This question first arose with the discovery of viruses. When the world was classifying everything under either Animal or Plant kingdoms (Two Kingdom Classification), there came these strange "living chemicals"; they could be crystallized like salt and sugar. When dry crystallized viruses were dissolved in water, they would again regain their ability to infect the host cells. They had genetic material, could evolve and adapt but, if left all by themselves, they were nothing but chemicals! Thus, came the need to revamp and redefine the whole system. In the new Five-Kingdom classification by R H Whittaker, viruses were not included. Monera, Protista, Fungi, Plantae and Animalia were the five kingdoms of the Living World while the poor viruses were left alone. They are still considered "living chemicals" which were the "borderline" between living and non-living. Now, coming to your question- Their method of classification is separate from the Five-Kingdom system because of their exclusion from the whole system but they are also classified under the Hierarchy of Kingdom, phylum, class, order, family, genus and species. Here is how they are classified on the basis of the LHT System of Classification by Lwoff, Horne and Tournier (1962): PHYLUM: Vira TWO SUBPHYLA: Deoxyvira (DNA viruses) and Ribovira (RNA Viruses) Now, Deoxyvira has three classes: a) Deoxyhelica (helical symmetry) b) Deoxycubica (cubical symmetry) c) Deoxybinala (viruses with head and tail) Now, the class Deoxyhelica houses the Order: Chitovirales (enveloped) wherein lies the Family: Poxviridae - poxviruses In class Deoxycubica, there are two orders- Order: Haplovirales (no envelope) and Order: Peplovirales (mantle viruses). Haplovirales has five families based on the different number of capsomers (sub-units of the protective protein coat: capsid) Family: Microvidae has 12 capsomeres, Family: Parvoviridae- 32, Family: Paplloviridae- 72, Family: Adenoviridae- 2 and Family: Iridoviridae- 812 number of capsomers. Order Peplovirales has Family: Herpesviridae with 162 capsomeres (herpes viruses). Class Deoxybinala (head-tail, remember?) contains the order Urovirales which in turn has the important family of Phagoviridae (bacteriophages). Coming to the SUBPHYLUM- RIBOVIRA: There are two classes: Class Ribohelica (helical symmetry) and Class Ribocubica (cubical symmetry). Class Ribohelica has two Orders: Order Rhabdovirales (rod-like viruses) and order Sagovirales. There are two sub-orders to Rhabdovirales: a) Rigidovirales Plant viruses and b) Flexiviridales Plant viruses Suborder : Rigidovirales Plant viruses has three families: Family: Dolichoviridae- 12-13 nm, Family :Protoviridae- 15 nm and Family : Pachyviridae 20 nm. The suborder Flexiviridales P.V. also has three families: Family: Leptoviridae- 10-11 nm, Family: Mesoviridae 12-13 nm, Family: Adroviridae 15 nm. The last order Sagovirales in the class Ribohelica also has three families: Family: Myxoviridae, Family: Paramyxoviridae, Family: Stomatoviridae I hope the above info along with all the details helped to clear up your doubts. Please feel free to ask any further questions on the topic. I will try and answer with the best of my capability. Thanks for asking.

What is the difference between the six levels of structural hierarchy in a protein?
I'm confused in understanding the concepts of the supersecondary (motif) structure, the domain structure, and how they all fit together with the primary structure, secondary structure, tertiary structure, and quaternary structure. I'm also confused on the organization of proteins based on motifs (such as alpha, beta, alpha/beta, alpha+beta). Thanks!

Biology is a wonderful science where things exist and we try to categorize it and label it, even when things are gray. Primary structure is easy, it is literally the sequence of the amino acids. motifs are what forms from the primary structure. Alpha helices will form with a certain sequence because the amino acids hydrogen bond in a specific manner. Same with Beta-pleated sheets. Therefore, the primary sequence induces the motifs. This is also called "secondary structure." The domain structure is how a clump or a section of the protein is organized. Basically, if the protein looks like it can be split into different sections, then these sections are called domains. The domains are considered tertiary structure. Basically they are what happens to the alpha helices and beta pleated sheets on a larger scale. For example, three seperate alpha-helices fold up to form a massive Y shape. Quaternary structure is how each of the domains fit together. I'm really not sure what you mean by the last questions, but it sounds like you're confused about the sequence of alpha and beta? I hope this all helped

How can a protein with no signal peptide be integrated into the plasma membrane as a transmembrane protien?
I am studying a protein in Neurospora crassa known as prm1. This protein has been identified in yeast as a transmembrane glycoprotein involved in cell fusion (it is a homolog to N. crassa prm1). Its method of action seems to be the stablaization of membrane pores that allow for cell fusion, and in its absence cell fusion of yeast can still occur. From computer predictions prm1 in N. crassa appears to have 5-6 transmembrane domains, however no signal peptide has been predicted from any program. How could this protein become integrated into the endomembrane system and later the plasma membrane if it lacks a signal peptide?

I know there are some proteins produced by prokaryotes and eukaryotes that lack a typical leader peptide sequence; for example lacking a hydrophobic leader peptide. Some of these proteins are exported to the membrane by a substrate specific ATP-driven membrane translocater. Used to be called ABC-transporters because they could bind and hydrolize ATP. I think T-cell presentation is associated with a system like this where ABC-transporters transport endogenous antigenic peptides to the ER where they bind to the MHC: peptide receptor complex before being transported to the cell surface. I know S. cerevisiae, MATa haploid cells, release a 12-residue posttranslationally modified lipopeptide that binds via a farnesyl moiety attached via a thioether linkage to the C-terminal residue. So, basically I would suggest looking at a possible ABC-transporter or a lipopeptide. There might be other options but they escape me at the moment.

If given the cDNA-deduced sequence, how do you know whether the protein is exported or domestic one?
How would I use hydropathy to locate the transmembrane domain? And what would most likely be the mature sequence? How would you figure that out?

you would have to decode the codon, and then fid out the name of the protein, match it to its usage and then deduced where it is used.