Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.
Full Answer
What is an example of a structural domain?
Structural domains. Although a protein domain may be generally associated with a family of proteins with related functions, it also may be found in proteins with very different functions. One such example is the hemopexin-related proteins.
What is a domain of a protein?
Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.
What is domain prediction in protein structure and function prediction?
Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods.
How does the structure of a protein relate to its function?
The structure of a protein is caused by the chemical properties of its amino acids. Insulin, a protein, has a specific amino acid sequence, which then causes a specific structure. This structure influences its function, which is to aid glucose in entering cells.
What is a domain in a protein How does it relate to structure and or function?
Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.
What do protein domains tell us?
Protein domains are the basic units of proteins that can fold, function, and evolve independently. Knowledge of protein domains is critical for protein classification, understanding their biological functions, annotating their evolutionary mechanisms and protein design.
What is a domain protein structure?
A protein domain is a region of the protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains. One domain may appear in a variety of different proteins.
How does the structure of a protein determine its function?
The unique amino acid sequence of a protein is reflected in its unique folded structure. This structure, in turn, determines the protein's function. This is why mutations that alter amino acid sequence can affect the function of a protein.
Which of the following best describes a protein domain?
What of the following best describes a protein domain? A relatively large pattern of three-dimensional structure that is recognized across many proteins.
How do you find the functional domain of a protein?
Use the CD-Search tool to identify conserved domains, or functional units, within a protein query sequence:Enter the protein query sequence, either as raw sequence data in FASTA format, or as a GI or Accession.More items...
What is a domain structure?
Domain structure. A complete domain name is known as a fully qualified domain name (FQDN). A FQDN states the exact position of a target computer within the tree hierarchy of the domain name system and is made up of two parts: the host name and the domain name. The following example is a fictitious mail server's FQDN.
What is the meaning of functional domain?
The functional domain is defined by the constraints on what can be expressed within the language and without elaboration. It determines the processing details that users may leave out of their expressions.
What is the main difference between protein domains and protein subunits?
A protein subunit is a separate polypeptide chain of a protein that assembles with other polypeptide chains to form a protein complex. On the other hand, the protein domain is a region of the polypeptide chain of protein that is self-stabilising and folds independently from the rest.
What are the four structural levels of proteins which determine its shape and function?
To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.
What is a protein domain quizlet?
Domain. Domain - protein region that can evolve, fold, and often function independently of the rest of the protein. Forms distinct 3D structure that is typically stable when isolated from intact protein. Often fairly large. Motif.
What is the main difference between protein domains and protein subunits?
A protein subunit is a separate polypeptide chain of a protein that assembles with other polypeptide chains to form a protein complex. On the other hand, the protein domain is a region of the polypeptide chain of protein that is self-stabilising and folds independently from the rest.
Why is domain considered as an evolutionary unit in proteins?
The suggestion was that each domain was an independent folding unit. Moreover, certain domains were associated with a particular function, such as NAD binding, and thus these domains were considered an evolutionary unit.
What did anfinsen's experiment show?
Anfinsen's experiment showed that the native structure of ribonuclease A will form following denaturation provided that premature oxidation is prevented. Therefore, the protein is intrinsically capable of finding its lowest-energy conformation.
What is a domain in a protein?
What are protein domains? Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein. Domains may exist in a variety of biological contexts, where similar domains can be found in proteins with different functions.
Which protein has multiple SH3 domains?
An example of a protein that contains multiple SH3 domains is the cytoplasmic protein Nck. Nck belongs to the adaptor family of proteins and it is involved in transducing signals from growth factor receptor tyrosine kinases to downstream signal recipients. The domain composition of Nck is illustrated in Figure 5.
What is the domain of Nck?
Figure 5 Domain composition of Nck. Nck contains three SH3 domains plus another domain known as SH2 (Src homology 2). Both SH3 and SH2 domains are usually found in proteins that interact with other proteins and mediate assembly of protein complexes. SH3 domains typically bind to proline-rich peptides in their respective binding partners, while SH2 domains interact with phosphotyrosine-containing target peptides.
How many SH3 domains are in Nck?
Nck contains three SH3 domains plus another domain known as SH2 (Src homology 2). Both SH3 and SH2 domains are usually found in proteins that interact with other proteins and mediate assembly of protein complexes.
Why is the chapter titled "Protein Structure and Function"?
This chapter is titled “protein structure and function” because protein structure heavily influences its function. The structure of a protein is caused by the chemical properties of its amino acids.
Why is the shape of a protein important?
As mentioned above, a protein’s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate.
How many amino acids are in a polypeptide chain?
A polypeptide chain is chain composed of amino acids. There are 20 amino acids commonly found in organisms.
Why are amino acids essential?
Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. Below are two illustrations depicting the relationship between amino acids and polypeptides. A protein is composed of polypeptide chain (s) and a polypeptide chain is made of amino acids.
How many proteins are in a cell?
Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence (also referred to as a “peptide”). Protein types and functions:
What is the function of insulin?
Insulin, a protein, has a specific amino acid sequence, which then causes a specific structure. This structure influences its function, which is to aid glucose in entering cells.
Which amino acid binds with other amino acids?
Negatively charged amino acids bind with positively charged amino acids (neutrally charged amino acids are not affected). Also, the amino acid called cysteine contains sulfur and sulfurs easily bind with each other, creating a “disulfide bond.”. Because of this, cysteines bind with other cysteines.
What is the function of proteins?
Analyzing Protein Structure and Function. Proteins perform most of the work of living cells. This versatile class of macromoleculeis involved in virtually every cellular process: proteins replicate and transcribe DNA, and produce, process, and secrete other proteins. They control cell division, metabolism, and the flow of materials ...
What do proteins do in a cell?
They control cell division, metabolism, and the flow of materials and information into and out of the cell. Understanding how cells work requires understanding how proteins function. The question of what a proteindoes inside a living cell is not a simple one to answer.
How does GFP work?
GFP, and its derivatives of different color, can also be used to monitor protein-protein interactions. In this application, two proteins of interest are each labeled with a different fluorochrome, such that the emission spectrum of one fluorochrome overlaps the absorption spectrum of the second fluorochrome. If the two proteins—and their attached fluorochromes—come very close to each other (within about 1–10 nm), the energy of the absorbed light will be transferred from one fluorochrome to the other. The energy transfer, called fluorescence resonance energy transfer (FRET), is determinedby illuminating the first fluorochrome and measuring emission from the second (Figure 8-49). By using two different spectral variants of GFP as the fluorochromes in such studies, one can monitor the interaction of any two protein molecules inside a living cell.
How to track proteins in cells?
Today large numbers of proteins are being tracked in living cells by using a fluorescent marker called green fluorescent protein(GFP). Tagging proteins with GFP is as simple as attaching the genefor GFP to one end of the gene that encodes a proteinof interest. In most cases, the resulting GFP fusion protein behaves in the same way as the original protein, and its movement can be monitored by following its fluorescence inside the cell by fluorescence microscopy. The GFP fusion protein strategy has become a standard way to determine the distribution and dynamics of any protein of interest in living cells. We discuss its use further in Chapter 9.
How many proteins are in the atomic model?
138–139). The three-dimensional structures of about 10,000 different proteins have now been determinedby x-ray crystallography or by NMRspectroscopy (see below)—enough to begin to see families of common structures emerging. These structures or protein folds often seem to be more conserved in evolution than are the amino acidsequences that form them (see Figure 3-15).
How to search for homologous sequences?
Searching a collection of known sequences for homologousgenes or proteins is typically done over the World-Wide Web, and it simply involves selecting a database and entering the desired sequence. A sequence alignment program—the most popular are BLAST and FASTA—scans the database for similar sequences by sliding the submitted sequence along the archived sequences until a cluster of residues falls into full or partial alignment (Figure 8-47). The results of even a complexsearch—which can be performed on either a nucleotideor an amino acidsequence—are returned within minutes. Such comparisons can be used to predict the functions of individual proteins, families of proteins, or even the entire proteincomplement of a newly sequenced organism.
Where do protein-protein interactions occur?
Although the protein-protein interactions occur in the yeastcell nucleus, proteins from every part of the cell and from any organism can be studied in this way. Of the thousands of protein-protein interactions that have been catalogued in yeast, half have been discovered with such two-hybrid screens.
What are the functions of protein domains?
Proteins domains are not limited to serving as mediators of interactions, but can also provide enzymatic functions . In eukaryotes, protein phosphorylation is a common posttranslational modification in up to 30% of cellular proteins ( Ubersax and Ferrell, 2007 ). Although phosphorylation occurs in a diverse range of proteins and amino acid sequence contexts, all protein kinases share a conserved three-dimensional structure defined by a canonical catalytic domain of approximately 250 amino acids ( Ubersax and Ferrell, 2007 ). The specificity for tyrosine versus serine/threonine is determined by the depth of the active site cleft with additional structure features, including various protein interaction domains, leading to proximal and distal determinants of substrate recognition ( Ubersax and Ferrell, 2007 ). Although not as abundant as kinases, protein phosphatases also share a common catalytic domain fold with combinatorial interaction between shared catalytic subunits and one of a large number of regulatory subunits to provide target specificity ( Shi, 2009 ).
Which proteins regulate transcription?
BET proteins regulate transcription of different herpesviruses, including Epstein–Barr virus and Kaposi’s sarcoma–associated herpesvirus, as well as papillomaviruses (reviewed in Weidner-Glunde et al., 2010).
What is the role of SRO in a protein?
SRO family members act as scaffolds bringing together TFs bound to their RST domains with other proteins. Members that contain WWE domains may recruit chromatin remodelling complexes through their WWE domains, and through the RST domain recruit several different TFs, especially those involved in abiotic stress response. The type of TFs bound by RCD1 and SRO family members are diverse, including members of the bZIP, WRKY, bHLH, HSF and AP2/ERF families ( Broché et al., 2014 ).
What is the Sun domain?
SUN domain proteins constitute an evolutionarily conserved family of proteins that share a common C-terminal motif, the so-called SUN (Sad1p/Unc84 homology) domain ( Hagan & Yanagida, 1995; Malone, Fixsen, Horvitz, & Han, 1999 ). As emphasized by the InterPro Database (InterPro Entry: IPR012919; http://www.ebi.ac.uk/interpro ), representatives of this family can be found in nearly all (if not all) eukaryotic taxa, from protists up to higher vertebrates (for selected examples, see Table 5.1 ). SUN domain proteins are integral membrane proteins of the INM with a single TM domain separating an N-terminal nucleoplasmic region from the C-terminal part that extends into the perinuclear space (PNS) ( Hodzic, Yeater, Bengtsson, Otto, & Stahl, 2004; Padmakumar et al., 2005 ). Though their N-terminal nucleoplasmic domains are not conserved, most family members nonetheless show remarkable conserved binding to nucleoskeletal elements and chromatin. SUN proteins directly interact with the KASH (Klarsicht/Anc1/Syne1 homology) domain of respective KASH protein partners within the PNS via their C-terminal SUN domain to form a complex that bridges both nuclear membranes ( McGee, Rillo, Anderson, & Starr, 2006; Sosa, Rothballer, Kutay, & Schwartz, 2012; Starr & Fischer, 2005; Starr & Fridolfsson, 2010 ). The KASH partners in turn are typically large proteins that contain a short, conserved C-terminal domain, the so-called KASH domain, which marks the defining feature of this protein family. KASH domains consist of a hydrophobic region spanning the ONM and a short, 6–30-residue-long sequence at the very C-terminal end that extends into the PNS and is designed to bind SUN domains. The large N-terminal domains of KASH proteins, however, are highly divergent and perform a variety of distinct functions, including centrosome attachment, nuclear migration, and tethering nuclei to different cytoskeletal elements ( Razafsky & Hodzic, 2009; Starr, 2009; Starr & Fischer, 2005 ).
Where are the KASH domains located?
KASH-domain proteins are single-pass transmembrane proteins that reside in the ONM. The bulk of these proteins protrude into the cytoplasm and different family members exhibit significant diversity in these cytoplasmic domains. However, the ~ 50 C-terminal amino acids that form the transmembrane and KASH domains exhibit high homology, not only among KASH-domain protein family members of a single species but also across different species. Indeed some key residues are conserved across kingdoms ( Fig. 6.2 from Sosa et al., 2013 ). The KASH-domain resides in the PNS where it interacts with SUN-domain proteins. The SUN (Sad-1 UNC-84) domain of these eponymous proteins is located at the C-terminus for most SUN proteins, while the N-terminus resides in the nucleoplasm and interacts with chromatin, other INM proteins, and components of the lamina. Five different SUN proteins have been identified in mammals, all of which are single-pass type II transmembrane proteins ( Rothballer & Kutay, 2013 ).
What are LEM domain proteins?
Their LEM domain directly recognizes the DNA-binding protein BAF ( Cai et al., 2001 ). However, these proteins are membrane proteins and their soluble regions are largely predicted as intrinsically disordered. LAP2α dimerizes through its C-terminal α-helical domain ( Bradley et al., 2007 ). Emerin also self-assembles into poorly characterized oligomers ( Berk et al., 2014 ). It is thus difficult to identify their functional states in vitro and to reconstitute complexes between these proteins and their biological partners. First attempts to stabilize NE complexes have recently led to the resolution of the X-ray structure of the KASH–SUN complex, located between the outer and INMs ( Sosa, Rothballer, Kutay, & Schwartz, 2012 ). Moreover, development of mass spectrometry and NMR techniques now enables description of posttranslational modification events in LEM-domain proteins, and their consequences on protein structure and binding properties. Integrative approaches, including structural characterization of protein subcomplexes based on a panel of biophysical techniques and development of new tools in biochemistry and imaging techniques for identification of protein–protein interfaces might ultimately provide a better view of inner NE architecture.
What is the role of LINC complexes in meiosis?
Besides their primary function in connecting nucleoplasmic to cytoplasmic structures, LINC complexes are crucial not only for dynamic processes, such as anchorage and migration of entire nuclei, but also for positioning and movement of nuclear structures ( Starr & Fridolfsson, 2010 ). Most striking is their role in meiosis, where SUN–KASH bridges serve as specific NE docking sites for meiotic telomeres, mediating the characteristic movements of chromosomes that are essential for meiotic chromosome pairing, synapsis, and recombination ( Alsheimer, 2009; Chi et al., 2009; Ding et al., 2007; Penkner et al., 2007; Schmitt et al., 2007; Shimanuki et al., 1997 ). Beyond that, a number of recent studies have provided strong evidence that LINC complexes play a most central role in nuclear deformation and shaping ( Oda & Fukuda, 2011; Olins et al., 2009; Xiong et al., 2008; Zhou, Graumann, Evans, & Meier, 2012 ). Previous reports suggested that during sperm differentiation, major forces guiding the characteristic elongation and shaping of the sperm head act from the cytoplasm ( Kierszenbaum, Rivkin, & Tres, 2003a, 2003b; Mendoza-Lujambio et al., 2002 ). In light of this, LINC complexes are expected to be key players for well-directed nuclear shaping in that they function as primary connectors to transfer these forces to the nucleus ( Göb et al., 2010; Kierszenbaum et al., 2011; Kracklauer et al., 2010 ).
What are some examples of protein domains?
One example is the vitamin-K-dependent modification of glutamates in coagulation factors and related proteins.
Where are kinase domains found?
Protein kinase domains are found in proteins that vary greatly in structure. An extreme example is the kinase domain in TTN (titin; also several other isoforms; see Muscle ), the largest human protein. Although such domains are generally easy to locate by sequence similarity, largely unrelated sequences may have similar types of activities, as is observed with the RIO kinases .
Which family of proteins requires dimerization?
The ATP-binding cassette family includes half transporters that require dimerization for function and larger proteins that contain an internal duplicated region.
Can proteins be parsed?
Many proteins can be readily parsed by sequence similarity into domains with specific functions. Other domains are defined by a relatively small number of noncontiguous, conserved residues, in some cases with variable spacing. Members of these families may be missed with searches using programs like BLASTP but detected with other pattern-matching methods.
Overview
Traits
- A trait is a specific characteristic of an organism, such as eye color or blood type. Traits can be determined by genes or the environment, or more commonly by interactions between them. The genetic contribution (i.e., the DNA) to a trait is called the genotype. The outward expression of the genotype, including visible and physiological traits, is called the phenotype.
Proteins
- Proteins are coded and regulated by genes. These proteins, along with the environment, cause an organism’s traits. Proteinsare one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or the…
Monomers and Polymers
- Monomers are molecules that can bind into long chains—these long chains are called “polymers.” In other words, a polymer (“poly” = many) are made of monomers (“mono” meaning “one”). Amino acidsare the monomers that comprise polypeptides (polypeptides being the polymers). A polypeptide folds into a 3D structure called a protein. Scientists use the name “amino acid” beca…
Protein Structure
- As mentioned above, a protein’s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the fou…
Mutations
- Mutations can impact protein synthesis and amino acid sequence. If these mutations are heritable, then they may influence the evolution of a species. Therefore, this chapter includes information on mutations and evolution.
Attributions
- This chapter is a modified derivative of the following articles: “Biological Molecules” by OpenStax College, Biology, CC BY 4.0. Download the original article for free at https://openstax.org/books/biology-2e/pages/3-4-proteins “Trait” by National Human Genome Research Institute, National Institutes of Health, Talking Glossary of Genetic Terms. Understandi…