Secondary structure prediction of protamines

Cid, Hilda; Arellano, Alejandro

doi:10.1016/0141-8130(82)90003-4

Cited by 16 publications

(7 citation statements)

References 15 publications

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“…It was noted that for the ␤-turns the most frequent pattern of residues observed is in the following form: hydrophobichydriphilic-hydrophilic-hydrophobic (57). Also, when a tetrapeptide is folding into a ␤-turn, the interaction between its first and fourth residues and the interaction between its second and third residues have become remarkable.…”

Section: -4 and 2-3 Residue-correlation Model (37)mentioning

confidence: 95%

Prediction of Tight Turns and Their Types in Proteins

Chou¹

2000

Analytical Biochemistry

259

197

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Section: -4 and 2-3 Residue-correlation Model (37)mentioning

confidence: 95%

Prediction of Tight Turns and Their Types in Proteins

Chou¹

2000

Analytical Biochemistry

259

197

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“…However, fish protamines tend to be under 35 amino acids in length and contain increased frequencies of arginine (approximately 70%) in comparison to their mammalian analogs. The secondary structure of the protamines consist of multiple beta turns, with limited CD, NMR, and fluorescence data, indicating the formation of a possible globular structure [10,11].…”

Section: Introductionmentioning

confidence: 99%

Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines

et al. 2020

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Background: Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra-and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. Results: Protamine sequences from UniProt's databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. Conclusions: High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. Also, the human protamine P1 sequence has a tyrosine substitution in a position expecting eutherian dicysteine cross-linking. Similarly, some members of the metatherian Planigales genus contain cysteine substitutions in positions expecting plausible metatherian dityrosine cross-linking. Rare cysteine-tyrosine cross-linking could explain both observations.

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“…(37,38) Similarly, it has been shown that basic N tails of histones H3 and H4 are ␣-helical when bound to DNA in the core particle and become unstructured in the unbound state. (39) However, secondary structure predictions according to Chou and Fasman do not support the high helical content of the protamine (14,40) and point to the essential role of turns and ␤-structure instead.…”

Section: Structural Datamentioning

confidence: 90%

“…It follows that it is not the considerations concerning the secondary structure of protamine but rather the turns of the chain due to the presence of proline and glycine residues, and intramolecular interactions that shape the the tertiary structure of the molecule. (14,17,58) In contrast to the earlier view, it could be imagined that the conformation of oligoarginine stretches is relatively free and could be adjusted when bound to DNA. In short, it can be supposed that nonbasic amino acids determine the internal structure of the protamine molecule, whereas basic residues are responsible for the interaction with DNA.…”

Section: Structural Datamentioning

confidence: 91%