Secondary structure

Biochemical terms

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The secondary structure used to be composed of biological macromolecules Atomic weight Level structure hydrogen bond To define. stay protein The secondary structure is based on the main chain amino Is defined by the mode of hydrogen bonding between, that is DSSP The hydrogen bond defined does not include the hydrogen bond between the main chain and the side chain or between the side chains. The secondary structure of nucleic acid is Base Is defined by the hydrogen bond between them. In many RNA molecules, the secondary structure is very important for the normal function of RNA, sometimes even more important than the sequence. This can be used for analysis Non coding RNA 。 RNA secondary structure can be improved by computer Forecast accuracy 。 Other bioinformatics applications will use some concepts of secondary structure to analyze RNA 。

Chinese name: Secondary structure
Foreign name: secondary structure

Discipline: biochemistry
Meaning: Biomacromolecule

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Basic concepts

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Secondary structure biochemistry and Structural Biology Middle refers to a biological giant molecule, such as protein and nucleic acid（ DNA or RNA ）, three-dimensional general formula of local sections. It does not describe any specific atomic position, which will be Tertiary structure Processing in.

detailed information

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Since hydrogen bond is related to other structural features, the secondary structure defined by it will be slightly informal. Like the protein helix, the main chain is usually used in the specific area of Raman strong label mapping Dihedral angle 。 Thus, the segment with this dihedral angle will be called "spiral", regardless of whether it is really hydrogen bonded or not. Other slightly informal definitions have also been suggested, and most of them are application curves differential geometry Concepts, such as curvature and Torsion 。 The most informal is Structural Biology The secondary structure of atomic scale is determined and recorded by the naked eye.

The secondary structure of biological macromolecules can be preliminarily estimated by spectrum. A common method for protein is called long ultraviolet rays (wavelength 170-250nm) circular dichroism. It can be displayed at the double minimum 208nm and 222nm Alpha helix The single smallest 204nm or 207nm can display arbitrary shape or Beta folding Structure. A less commonly used method is infrared Spectrum, which can detect the cause hydrogen bond The shock of amino group caused. Finally, the secondary structure can accurately nuclear magnetic resonance Of chemical shift To estimate.

number

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DSSP Is the abbreviation of "Define Secondary Structure of Proteins", which is an article formally listing known three-dimensional structure Of Protein secondary structure 。 The DSSP number is usually a single English letter To describe the secondary structure of protein. The secondary structure is based on hydrogen bond Mode.

*G: 3 angle spiral (i.e. 310 spiral). The minimum length is 3 Residue 。

*H: 4 angle spiral（ Alpha helix ）。 The minimum length is 4 residues.

*I: 5 angle spiral (π spiral). The minimum length is 5 residues.

*T: hydrogen bond corners (3, 4 or 5 corners).

*E: Parallel Beta folding , or/and antiparallel folded form (extended chain). The shortest length is 2 residues.

*B: Residues in independent β bridges (a pair of β folds hydrogen bond ）

*S: Bending (designation of unique non hydrogen bond)

All residues not in the above form DSSP They are specified by spaces, and sometimes C represents curl or L represents ring. Spiral (i.e. G, H and I) and folded form all need certain length. This means that the two Primary structure Adjacent residues must form the same hydrogen bonding pattern. If the spiral or folded hydrogen bond mode is too short, it will be coded with T or B respectively. There are others Protein secondary structure Number, but less used.

protein Secondary structure prediction

early stage protein The method of secondary structure prediction is based on amino acid The tendency to form spirals or folds is sometimes used in conjunction with the method of estimating the energy to form a secondary structure. These methods can predict about 60% of residues in three states (spiral, folded or curled) accuracy , if used Multiple sequence alignment The accuracy can be greatly improved to 80%. Multiple sequence alignment can know the complete distribution of amino acids at a certain position (including the position near it, generally 7 residues on each side), and the evolution process provides a clearer picture of the structural trend. For example, the glycine in a certain position of the protein itself has shown that it is an arbitrary shape. However, multiple sequence comparison can find that in 95% of the proteins after nearly a billion years of evolution, that is a favorable helical amino acid. Furthermore, if the average is detected at that position Hydrophobicity It will also be found that the residue solubility is related to Alpha helix agreement. Taken together, these factors indicate that the original protein endogenous glycine is Alpha helical structure , not arbitrary. Various methods will combine the existing data to form the prediction of three states. These methods include neural network hidden Markov model and Support vector machine 。 modern Prediction method It can also provide confidence scores in the prediction results of each location.

Secondary structure prediction The method has been continuously calibrated, such as EVA experiment. Based on the 270 week test, the most accurate methods are PsiPRED, SAM, PORTER, PROF and SABLE. Interestingly, finding consensus or consistency among these methods does not improve their accuracy. The biggest improvement seems to be in the prediction of beta stocks, because the method used will ignore some beta stocks. Overall, the highest Forecast accuracy It can only reach 90%, because DSSP standard method The nature of is contrary to the calibrated prediction.

accurate Secondary structure prediction yes Tertiary structure An important element of prediction. For example, a certain beta beta beta beta secondary Structure mode Is the mark of iron redox protein.

protein

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Secondary structure of protein Including local residues hydrogen bond Regulated interactions. The most common secondary structure is Alpha helix and Beta folding , plus β - angle And random crimping. After calculation, it is found that other helices, such as 310 helices and π helices, have favorable hydrogen bonding modes in energy, but these helices are rare in natural proteins Alpha helix It can only be found in the end after unfavorable skeleton packaging is carried out in the center. Tight corners, loose and flexible rings will connect more "regular" secondary structures. Arbitrary form is not a true secondary structure, but it is a form of secondary structure lacking rules.

amino acid They have different abilities in forming different secondary structures. proline and glycine It will appear on the corner and can disrupt the regular form of the alpha spiral skeleton, but both have abnormal morphological ability. The amino acids in helical form in protein are methionine 、 alanine 、 leucine 、 glutamate and Lysine (The single letter number of amino acid is "MALEK"); In contrast, large Aromaticity Residue（ Tryptophan 、 Tyrosine and Phenylalanine ）And C β branched amino acids（ isoleucine 、 valine and threonine ）Then use Beta folding form. However, these are not enough to form a reliable method to predict the secondary structure in terms of sequences alone.

nucleic acid

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Nucleic acid also has a secondary structure, most of which are single strand Ribonucleic acid (RNA) molecule. RNA secondary structure can be divided into spiral ( Base pair ）And different kinds of rings (unpaired ones surrounded by spirals nucleotide ）。 Stem ring structure Is a base pair Helical structure , the end is a short unpaired ring. This kind of stem ring structure is very common, and it is a large Structural primitive , such as Clover structure (i.e. as in Transport RNA Four spiral nodes in) Basic unit 。 Inner ring structure (short and unpaired in long base pair helix Base ）And bulging (extra insertion in the spiral strand, but no paired base in the relative strand) are also very common. Finally, pseudoknots and base triples also appear in RNA.

Since almost all RNA secondary structures are mediated by base pairs, it can be said to determine which base pairs are in a molecule or complex. However, the traditional Watson Crick Base pair It is not the only pairing method in RNA, but the Hochsler pairing method is also very common.

application

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One application of bioinformatics is to use predicted RNA secondary structures to search for RNA functional forms rather than codes genome 。 For example, Small RNA It has the length interrupted by the small inner ring Stem ring structure 。 The calculation of possible RNA secondary structures can be performed by dynamic programming Method, but it cannot detect false knots or other Base pair In the case of no comprehensive coverage, the general method is random context Unrelated syntax. Mfold is a website that uses dynamic planning.

comparison

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Both protein and RNA secondary structures can be used to assist Multiple sequence alignment 。 This comparison can become more accurate after adding relevant secondary structure data. But sometimes it is not very useful for RNA, because RNA Base The comparison sequence is highly preserved. For some proteins that cannot be compared with the primary structure, the secondary structure can sometimes be found out the relationship between them.

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