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70-610: ORF8 in SARS-CoV-2 encodes a protein of 121 amino acid residues with an N-terminal signal sequence . ORF8 forms a dimer that is covalently linked by disulfide bonds . It has an immunoglobulin-like domain with distant similarity to the ORF7a protein. Despite a similar overall fold, an insertion in ORF8 likely is responsible for different protein-protein interactions and creates an additional dimerization interface. Unlike ORF7a, ORF8 lacks

140-437: A dimer if it contains two subunits, a trimer if it contains three subunits, a tetramer if it contains four subunits, and a pentamer if it contains five subunits, and so forth. The subunits are frequently related to one another by symmetry operations , such as a 2-fold axis in a dimer. Multimers made up of identical subunits are referred to with a prefix of "homo-" and those made up of different subunits are referred to with

210-649: A helix bundle , β-barrel , Rossmann fold or different "folds" provided in the Structural Classification of Proteins database . A related concept is protein topology . Proteins are not static objects, but rather populate ensembles of conformational states . Transitions between these states typically occur on nanoscales , and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis . Protein dynamics and conformational changes allow proteins to function as nanoscale biological machines within cells, often in

280-447: A protein family . RNA secondary structure Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA

350-473: A residue , which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions , in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond . By convention, a chain under 30 amino acids is often identified as a peptide , rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by

420-510: A transmembrane helix and is therefore not a transmembrane protein , though it has been suggested it might have a membrane-anchored form. ORF8 in SARS-CoV and SARS-CoV-2 are very divergent, with less than 20% sequence identity . The full-length ORF8 in SARS-CoV encodes a protein of 122 residues. In many SARS-CoV isolates it is split into ORF8a and ORF8b, separately expressing 39-residue ORF8a and 84-residue ORF8b proteins. It has been suggested that

490-412: A " supersecondary unit ". Tertiary structure refers to the three-dimensional structure created by a single protein molecule (a single polypeptide chain ). It may include one or several domains . The α-helices and β-pleated-sheets are folded into a compact globular structure . The folding is driven by the non-specific hydrophobic interactions , the burial of hydrophobic residues from water , but

560-455: A class of doubly ringed chemical structures called purines ; the smaller nucleobases, cytosine and thymine (and uracil), are members of a class of singly ringed chemical structures called pyrimidines . Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because

630-409: A large number of different proteins Tertiary protein structures can have multiple secondary elements on the same polypeptide chain. The supersecondary structure refers to a specific combination of secondary structure elements, such as β-α-β units or a helix-turn-helix motif. Some of them may be also referred to as structural motifs. A protein fold refers to the general protein architecture, like

700-575: A longer paired helix) and bulges (regions in which one strand of a helix has "extra" inserted bases with no counterparts in the opposite strand) are also frequent. There are many secondary structure elements of functional importance to biological RNAs; some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf . Active research is on-going to determine the secondary structure of RNA molecules, with approaches including both experimental and computational methods (see also

770-400: A major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove. Many double-helical forms are possible; for DNA the three biologically relevant forms are A-DNA , B-DNA , and Z-DNA , while RNA double helices have structures similar to

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840-605: A nearest neighbor thermodynamic model. A common method to determine the most probable structures given a sequence of nucleotides makes use of a dynamic programming algorithm that seeks to find structures with low free energy. Dynamic programming algorithms often forbid pseudoknots , or other cases in which base pairs are not fully nested, as considering these structures becomes computationally very expensive for even small nucleic acid molecules. Other methods, such as stochastic context-free grammars can also be used to predict nucleic acid secondary structure. For many RNA molecules,

910-510: A number of non-covalent interactions , such as hydrogen bonding , ionic interactions , Van der Waals forces , and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure . This is the topic of the scientific field of structural biology , which employs techniques such as X-ray crystallography , NMR spectroscopy , cryo-electron microscopy (cryo-EM) and dual polarisation interferometry , to determine

980-430: A number of highly dynamic and partially unfolded proteins, such as Sic1 / Cdc4 , p15 PAF , MKK7 , Beta-synuclein and P27 As it is translated, polypeptides exit the ribosome mostly as a random coil and folds into its native state . The final structure of the protein chain is generally assumed to be determined by its amino acid sequence ( Anfinsen's dogma ). Thermodynamic stability of proteins represents

1050-518: A part of the primary structure, and cannot be read from the gene. For example, insulin is composed of 51 amino acids in 2 chains. One chain has 31 amino acids, and the other has 20 amino acids. Secondary structure refers to highly regular local sub-structures on the actual polypeptide backbone chain. Two main types of secondary structure, the α-helix and the β-strand or β-sheets , were suggested in 1951 by Linus Pauling . These secondary structures are defined by patterns of hydrogen bonds between

1120-560: A prefix of "hetero-", for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobin . An assemblage of multiple copies of a particular polypeptide chain can be described as a homomer , multimer or oligomer . Bertolini et al. in 2021 presented evidence that homomer formation may be driven by interaction between nascent polypeptide chains as they are translated from mRNA by nearby adjacent ribosomes . Hundreds of proteins have been identified as being assembled into homomers in human cells. The process of assembly

1190-517: A protein can be determined by methods such as Edman degradation or tandem mass spectrometry . Often, however, it is read directly from the sequence of the gene using the genetic code . It is strictly recommended to use the words "amino acid residues" when discussing proteins because when a peptide bond is formed, a water molecule is lost, and therefore proteins are made up of amino acid residues. Post-translational modifications such as phosphorylations and glycosylations are usually also considered

1260-464: A protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. Protein structure databases are critical for many efforts in computational biology such as structure based drug design , both in developing

1330-416: A representation of a protein that can be considered to have a flexible structure. Creating these files requires determining which of the various theoretically possible protein conformations actually exist. One approach is to apply computational algorithms to the protein data in order to try to determine the most likely set of conformations for an ensemble file. There are multiple methods for preparing data for

1400-463: A time and subjects all of them to experimental data. Here the experimental data is serving as limitations to be placed on the conformations (e.g. known distances between atoms). Only conformations that manage to remain within the limits set by the experimental data are accepted. This approach often applies large amounts of experimental data to the conformations which is a very computationally demanding task. The conformational ensembles were generated for

1470-430: A valuable method to investigate the structures of flexible peptides and proteins that cannot be studied with other methods. A more qualitative picture of protein structure is often obtained by proteolysis , which is also useful to screen for more crystallizable protein samples. Novel implementations of this approach, including fast parallel proteolysis (FASTpp) , can probe the structured fraction and its stability without

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1540-595: A variety of structures with catalytic activity and several important biological processes rely on RNA molecules that form pseudoknots. For example, the RNA component of the human telomerase contains a pseudoknot that is critical for its activity. The hepatitis delta virus ribozyme is a well known example of a catalytic RNA with a pseudoknot in its active site. Though DNA can also form pseudoknots, they are generally not present in standard physiological conditions . Most methods for nucleic acid secondary structure prediction rely on

1610-437: Is also possible that the absence of ORF8 reflects gene loss in those lineages. Amino acid residue Protein structure is the three-dimensional arrangement of atoms in an amino acid -chain molecule . Proteins are polymers  – specifically polypeptides  – formed from sequences of amino acids , which are the monomers of the polymer. A single amino acid monomer may also be called

1680-414: Is an element of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example,

1750-416: Is an important tertiary structure in nucleic acid molecules which is intimately connected with the molecule's secondary structure. A double helix is formed by regions of many consecutive base pairs. The nucleic acid double helix is a spiral polymer, usually right-handed, containing two nucleotide strands which base pair together. A single turn of the helix constitutes about ten nucleotides, and contains

1820-440: Is conflicting evidence on whether loss of ORF8 affects the efficiency of viral replication . A function often suggested for ORF8 protein is interacting with the host immune system . The SARS-CoV-2 protein is thought to have a role in immunomodulation via immune evasion or suppressing host immune responses. It has been reported to be a type I interferon antagonist and to downregulate class I MHC . The SARS-CoV-2 ORF8 protein

1890-535: Is highly immunogenic and high levels of antibodies to the protein have been found in patients with or recovered from COVID-19 . A study indicates that ORF8 is a transcription inhibitor . It has been suggested that the SARS-CoV ORF8a protein assembles into multimers and forms a viroporin . The evolutionary history of ORF8 is complex. It is among the least conserved regions of the Sarbecovirus genome. It

1960-427: Is no longer justified. Topology of a protein can be used to classify proteins as well. Knot theory and circuit topology are two topology frameworks developed for classification of protein folds based on chain crossing and intrachain contacts respectively. The generation of a protein sequence is much easier than the determination of a protein structure. However, the structure of a protein gives much more insight in

2030-618: Is often initiated by the interaction of the N-terminal region of polypeptide chains. Evidence that numerous gene products form homomers (multimers) in a variety of organisms based on intragenic complementation evidence was reviewed in 1965. Proteins are frequently described as consisting of several structural units. These units include domains, motifs , and folds. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are many fewer different domains, structural motifs and folds. A structural domain

2100-430: Is possible that ORF8 does not affect fitness in human hosts. In SARS-CoV, a high dN/dS ratio has been observed in ORF8, consistent with positive selection or with relaxed selection . ORF8 encodes a protein whose immunoglobulin domain (Ig) has distant similarity to that of ORF7a . It has been suggested that ORF8 likely have evolved from ORF7a through gene duplication , though some bioinformatics analyses suggest

2170-434: Is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing , since the pattern of basepairing ultimately determines

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2240-418: Is subject to frequent mutations and deletions, and has been described as "hypervariable" and a recombination hotspot . It has been suggested that RNA secondary structures in the region are associated with genomic instability . In SARS-CoV, the ORF8 region is thought to have originated through recombination among ancestral bat coronaviruses. Among the most distinctive features of this region in SARS-CoV

2310-536: Is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content , but contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly and stabilization is mainly due to stacking interactions. The larger nucleobases , adenine and guanine, are members of

2380-639: Is the emergence of a 29- nucleotide deletion that split the full-length open reading frame into two smaller ORFs, ORF8a and ORF8b. Viral isolates from early in the SARS epidemic have a full-length, intact ORF8, but the split structure emerged later in the epidemic. Similar split structures have since been observed in bat coronaviruses. Mutations and deletions have also been seen in SARS-CoV-2 variants . Based on observations in SARS-CoV, it has been suggested that changes in ORF8 may be related to host adaptation , but it

2450-516: Is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes , or physical force. Melting occurs preferentially at certain points in the nucleic acid. T and A rich sequences are more easily melted than C and G rich regions. Particular base steps are also susceptible to DNA melting, particularly T A and T G base steps. These mechanical features are reflected by

2520-502: Is typically lower than that of X-ray crystallography, or NMR, but the maximum resolution is steadily increasing. This technique is still a particularly valuable for very large protein complexes such as virus coat proteins and amyloid fibers. General secondary structure composition can be determined via circular dichroism . Vibrational spectroscopy can also be used to characterize the conformation of peptides, polypeptides, and proteins. Two-dimensional infrared spectroscopy has become

2590-525: The List of RNA structure prediction software ). A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots . The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes

2660-705: The Protein Ensemble Database that fall into two general methodologies – pool and molecular dynamics (MD) approaches (diagrammed in the figure). The pool based approach uses the protein's amino acid sequence to create a massive pool of random conformations. This pool is then subjected to more computational processing that creates a set of theoretical parameters for each conformation based on the structure. Conformational subsets from this pool whose average theoretical parameters closely match known experimental data for this protein are selected. The alternative molecular dynamics approach takes multiple random conformations at

2730-584: The U2AF2 protein, the splicing process is inhibited. However, in zebrafish and other teleosts the RNA splicing process can still occur on certain genes in the absence of U2AF2. This may be because 10% of genes in zebrafish have alternating TG and AC base pairs at the 3' splice site (3'ss) and 5' splice site (5'ss) respectively on each intron, which alters the secondary structure of the RNA. This suggests that secondary structure of RNA can influence splicing, potentially without

2800-418: The free energy difference between the folded and unfolded protein states. This free energy difference is very sensitive to temperature, hence a change in temperature may result in unfolding or denaturation. Protein denaturation may result in loss of function, and loss of native state. The free energy of stabilization of soluble globular proteins typically does not exceed 50 kJ/mol. Taking into consideration

2870-424: The mobile protein domains connected by them to recruit their binding partners and induce long-range allostery via protein domain dynamics . " Proteins are often thought of as relatively stable tertiary structures that experience conformational changes after being affected by interactions with other proteins or as a part of enzymatic activity. However, proteins may have varying degrees of stability, and some of

ORF8 - Misplaced Pages Continue

2940-402: The polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end (NH 2 -group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to

3010-520: The wobble base pair and Hoogsteen base pair , also occur—particularly in RNA—;giving rise to complex and functional tertiary structures . Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation . Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. Hydrogen bonding

3080-552: The " calcium -binding domain of calmodulin ". Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins. A conservative combination of several domains that occur in different proteins, such as protein tyrosine phosphatase domain and C2 domain pair, was called "a superdomain" that may evolve as a single unit. The structural and sequence motifs refer to short segments of protein three-dimensional structure or amino acid sequence that were found in

3150-479: The A form of DNA. The secondary structure of nucleic acid molecules can often be uniquely decomposed into stems and loops. The stem-loop structure (also often referred to as an "hairpin"), in which a base-paired helix ends in a short unpaired loop, is extremely common and is a building block for larger structural motifs such as cloverleaf structures, which are four-helix junctions such as those found in transfer RNA . Internal loops (a short series of unpaired bases in

3220-487: The ER. It is probably a secreted protein . There are variable reports in the literature regarding the localization of SARS-CoV ORF8a, ORF8b, or ORF8ab proteins. It is unclear if ORF8b is expressed at significant levels under natural conditions. The full-length ORF8ab appears to localize to the ER. The function of the ORF8 protein is unknown. It is not essential for viral replication in either SARS-CoV or SARS-CoV-2, though there

3290-550: The ORF8a and ORF8b proteins may form a protein complex . The cysteine residue responsible for dimerization of the SARS-CoV-2 protein is not conserved in the SARS-CoV sequence. The ORF8ab protein has also been reported to form disulfide-linked multimers . The full-length SARS-CoV ORF8ab protein is post-translationally modified by N-glycosylation , which is predicted to be conserved in the SARS-CoV-2 protein. Under experimental conditions, both 8b and 8ab are ubiquitinated . Along with

3360-429: The aggregation of two or more individual polypeptide chains (subunits) that operate as a single functional unit ( multimer ). The resulting multimer is stabilized by the same non-covalent interactions and disulfide bonds as in tertiary structure. There are many possible quaternary structure organisations. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers . Specifically it would be called

3430-422: The computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein. Protein structures can be grouped based on their structural similarity, topological class or a common evolutionary origin. The Structural Classification of Proteins database and CATH database provide two different structural classifications of proteins. When

3500-559: The form of multi-protein complexes . Examples include motor proteins , such as myosin , which is responsible for muscle contraction, kinesin , which moves cargo inside cells away from the nucleus along microtubules , and dynein , which moves cargo inside cells towards the nucleus and produces the axonemal beating of motile cilia and flagella . "[I]n effect, the [motile cilium] is a nanomachine composed of perhaps over 600 proteins in molecular complexes, many of which also function independently as nanomachines... Flexible linkers allow

3570-413: The function of the protein than its sequence. Therefore, a number of methods for the computational prediction of protein structure from its sequence have been developed. Ab initio prediction methods use just the sequence of the protein. Threading and homology modeling methods can build a 3-D model for a protein of unknown structure from experimental structures of evolutionarily-related proteins, called

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3640-417: The genes for other accessory proteins, the ORF8 gene is located near those encoding the structural proteins, at the 5' end of the coronavirus RNA genome. Along with ORF6 , ORF7a , and ORF7b , ORF8 is located between the membrane (M) and nucleocapsid (N) genes. The SARS-CoV-2 ORF8 protein has a signal sequence for trafficking to the endoplasmic reticulum (ER) and has been experimentally localized to

3710-475: The large number of hydrogen bonds that take place for the stabilization of secondary structures, and the stabilization of the inner core through hydrophobic interactions, the free energy of stabilization emerges as small difference between large numbers. Around 90% of the protein structures available in the Protein Data Bank have been determined by X-ray crystallography . This method allows one to measure

3780-468: The less stable variants are intrinsically disordered proteins . These proteins exist and function in a relatively 'disordered' state lacking a stable tertiary structure . As a result, they are difficult to describe by a single fixed tertiary structure . Conformational ensembles have been devised as a way to provide a more accurate and 'dynamic' representation of the conformational state of intrinsically disordered proteins . Protein ensemble files are

3850-593: The main-chain peptide groups. They have a regular geometry, being constrained to specific values of the dihedral angles ψ and φ on the Ramachandran plot . Both the α-helix and the β-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. Some parts of the protein are ordered but do not form any regular structures. They should not be confused with random coil , an unfolded polypeptide chain lacking any fixed three-dimensional structure. Several sequential secondary structures may form

3920-400: The molecules are too close, leading to overlap repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. The GU wobble base pair , with two hydrogen bonds, does occur fairly often in RNA . Hybridization is the process of complementary base pairs binding to form a double helix . Melting

3990-406: The need for purification. Once a protein's structure has been experimentally determined, further detailed studies can be done computationally, using molecular dynamic simulations of that structure. A protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate

4060-464: The overall structure of the molecules. In molecular biology , two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T) and guanine (G) forms one with cytosine (C) in DNA. In RNA, thymine is replaced by uracil (U). Alternate hydrogen bonding patterns, such as

4130-702: The phosphate backbone of one of the strands so that it can swivel around the other. Helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase . Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Frequently these elements, or combinations of them, are further classified into additional categories including, for example, tetraloops , pseudoknots , and stem-loops . Topological approaches can be used to categorize and compare complex structures that arise from combining these elements in various arrangements. The double helix

4200-513: The presence of general pseudoknots in nucleic acid sequences impossible to predict by the standard method of dynamic programming , which uses a recursive scoring system to identify paired stems and consequently cannot detect non-nested base pairs with common algorithms. However, limited subclasses of pseudoknots can be predicted using modified dynamic programs. Newer structure prediction techniques such as stochastic context-free grammars are also unable to consider pseudoknots. Pseudoknots can form

4270-405: The protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes 3D coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. Though most instances, in this case either proteins or a specific structure determinations of

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4340-466: The protein. A specific sequence of nucleotides in DNA is transcribed into mRNA , which is read by the ribosome in a process called translation . The sequence of amino acids in insulin was discovered by Frederick Sanger , establishing that proteins have defining amino acid sequences. The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of

4410-422: The same protein are referred to as different conformations , and transitions between them are called conformational changes . There are four distinct levels of protein structure. The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis . The two ends of

4480-587: The secondary structure is highly important to the correct function of the RNA — often more so than the actual sequence. This fact aids in the analysis of non-coding RNA sometimes termed "RNA genes". One application of bioinformatics uses predicted RNA secondary structures in searching a genome for noncoding but functional forms of RNA. For example, microRNAs have canonical long stem-loop structures interrupted by small internal loops. RNA secondary structure applies in RNA splicing in certain species. In humans and other tetrapods, it has been shown that without

4550-608: The similarity may be too low to support duplication, which is relatively uncommon in viruses. Immunoglobulin domains are uncommon in coronaviruses; other than the subset of betacoronaviruses with ORF8 and ORF7a, only a small number of bat alphacoronaviruses have been identified as containing likely Ig domains, while they are absent from gammacoronaviruses and deltacoronaviruses . ORF8 is notably absent in MERS-CoV . The beta and alpha Ig domains may be independent acquisitions, where ORF8 and ORF7a may have been acquired from host proteins. It

4620-530: The structural similarity is large the two proteins have possibly diverged from a common ancestor, and shared structure between proteins is considered evidence of homology . Structure similarity can then be used to group proteins together into protein superfamilies . If shared structure is significant but the fraction shared is small, the fragment shared may be the consequence of a more dramatic evolutionary event such as horizontal gene transfer , and joining proteins sharing these fragments into protein superfamilies

4690-439: The structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges , hydrogen bonds, and the tight packing of side chains and disulfide bonds . The disulfide bonds are extremely rare in cytosolic proteins, since the cytosol (intracellular fluid) is generally a reducing environment. Quaternary structure is the three-dimensional structure consisting of

4760-475: The structure of proteins. Protein structures range in size from tens to several thousand amino acids. By physical size, proteins are classified as nanoparticles , between 1–100 nm. Very large protein complexes can be formed from protein subunits . For example, many thousands of actin molecules assemble into a microfilament . A protein usually undergoes reversible structural changes in performing its biological function. The alternative structures of

4830-428: The three-dimensional (3-D) density distribution of electrons in the protein, in the crystallized state, and thereby infer the 3-D coordinates of all the atoms to be determined to a certain resolution. Roughly 7% of the known protein structures have been obtained by nuclear magnetic resonance (NMR) techniques. For larger protein complexes, cryo-electron microscopy can determine protein structures. The resolution

4900-566: The use of sequences such as TATAA at the start of many genes to assist RNA polymerase in melting the DNA for transcription. Strand separation by gentle heating, as used in PCR , is simple providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. The cell avoids this problem by allowing its DNA-melting enzymes ( helicases ) to work concurrently with topoisomerases , which can chemically cleave

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