Secondary structure of protamine in sperm nuclei: an infrared spectroscopy study.


BACKGROUND:Protamines are small basic proteins that condense the DNA in mature spermatozoa. Typical protamines are of simple composition and very arginine-rich, usually in the range of 60-80%. Arginine residues are distributed in a number of stretches separated by neutral amino acids. We have used Fourier transform infrared spectroscopy (FTIR) to gain access for the first time to the secondary structure of protamines in sperm nuclei. This technique is particularly well suited to the study of DNA-bound protamine in whole nuclei since it is not affected by turbidity. RESULTS:We show that DNA -bound salmon (salmine) and squid protamines contain α-helix, β-turns and a proportion of other structures not stabilized by intramolecular hydrogen bonding. No β-sheet was observed. In salmine, the α-helix amounted to ~20%, while in squid protamine it reached ~40%. In contrast, the structure not stabilized by intermolecular hydrogen bonding was more abundant in salmine (~40%) than in squid protamine (~20%). Both protamines contained ~40% β-turns. The different helical potential of salmine and squid protamine was confirmed by structure predictions and CD in the presence of trifluoroethanol. CONCLUSION:DNA-bound protamine in sperm nuclei contains large amounts of defined secondary structure stabilized by intramolecular hydrogen bonding. Both salmine and squid protamine contain similar amounts of β-turns, but differ in the proportions of α-helix and non-hydrogen bonded conformations. In spite of the large differences in the proportions of secondary structure motifs between salmon and squid protamines, they appear to be equally efficient in promoting tight hexagonal packing of the DNA molecules in sperm nuclei.


BMC Struct Biol


BMC structural biology


Roque A,Ponte I,Suau P




Has Abstract


2011-03-24 00:00:00










  • PDBalert: automatic, recurrent remote homology tracking and protein structure prediction.

    abstract:BACKGROUND:During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template). When...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Agarwal V,Remmert M,Biegert A,Söding J

    更新日期:2008-11-25 00:00:00

  • Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence.

    abstract:BACKGROUND:A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus tran...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Pahlke D,Freund C,Leitner D,Labudde D

    更新日期:2005-04-01 00:00:00

  • Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

    abstract:BACKGROUND:In the last decade, various coarse-grained elastic network models have been developed to study the large-scale motions of proteins and protein complexes where computer simulations using detailed all-atom models are not feasible. Among these models, the Gaussian Network Model (GNM) and Anisotropic Network Mod...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Lin TL,Song G

    更新日期:2010-05-17 00:00:00

  • Antibody-protein interactions: benchmark datasets and prediction tools evaluation.

    abstract:BACKGROUND:The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among the various methods of B-cell epitope identification X-ray crystallography is one of the most reliable methods. Using these experimenta...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Ponomarenko JV,Bourne PE

    更新日期:2007-10-02 00:00:00

  • Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome.

    abstract:BACKGROUND:Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16S rRNA. We are interested in evaluating the factors that might be responsible for restricting...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Huggins W,Ghosh SK,Wollenzien P

    更新日期:2009-07-30 00:00:00

  • Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type.

    abstract:BACKGROUND:A large number of studies have been carried out to obtain amino acid propensities for α-helices and β-sheets. The obtained propensities for α-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the β-sheet propensities obtained by several s...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Fujiwara K,Toda H,Ikeguchi M

    更新日期:2012-08-02 00:00:00

  • A three dimensional visualisation approach to protein heavy-atom structure reconstruction.

    abstract:BACKGROUND:A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates. RESULTS:We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy bac...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Peng X,Chenani A,Hu S,Zhou Y,Niemi AJ

    更新日期:2014-12-31 00:00:00

  • Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach.

    abstract:BACKGROUND:The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWI...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bouard C,Terreux R,Tissier A,Jacqueroud L,Vigneron A,Ansieau S,Puisieux A,Payen L

    更新日期:2017-05-18 00:00:00

  • Evolutionary traces decode molecular mechanism behind fast pace of myosin XI.

    abstract:BACKGROUND:Cytoplasmic class XI myosins are the fastest processive motors known. This class functions in high-velocity cytoplasmic streaming in various plant cells from algae to angiosperms. The velocities at which they process are ten times faster than its closest class V homologues. RESULTS:To provide sequence deter...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Syamaladevi DP,Sowdhamini R

    更新日期:2011-09-26 00:00:00

  • Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.

    abstract:BACKGROUND:Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Ku SY,Cornell KA,Howell PL

    更新日期:2007-10-25 00:00:00

  • Structure and characterization of a novel chicken biotin-binding protein A (BBP-A).

    abstract:BACKGROUND:The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Hytönen VP,Määttä JA,Niskanen EA,Huuskonen J,Helttunen KJ,Halling KK,Nordlund HR,Rissanen K,Johnson MS,Salminen TA,Kulomaa MS,Laitinen OH,Airenne TT

    更新日期:2007-03-07 00:00:00

  • Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: homology modelling and molecular dynamic studies.

    abstract:BACKGROUND:The coronavirus 3 chymotrypsin-like protease (3CL(pro)) is a validated target in the design of potential anticoronavirus inhibitors. The high degree of homology within the protease's active site and substrate conservation supports the identification of broad spectrum lead compounds. A previous study identifi...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Berry M,Fielding B,Gamieldien J

    更新日期:2015-04-28 00:00:00

  • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.

    abstract:BACKGROUND:How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of simi...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Keskin O

    更新日期:2007-05-17 00:00:00

  • The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.

    abstract:BACKGROUND:Ras-like GTPases function as on-off switches in intracellular signalling pathways and include the Rab, Rho/Rac, Ran, Ras, Arf, Sar and G alpha families. How these families have evolutionarily diverged from each other at the sequence level provides clues to underlying mechanisms associated with their function...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Neuwald AF

    更新日期:2009-03-05 00:00:00

  • Evolutionarily consistent families in SCOP: sequence, structure and function.

    abstract:BACKGROUND:SCOP is a hierarchical domain classification system for proteins of known structure. The superfamily level has a clear definition: Protein domains belong to the same superfamily if there is structural, functional and sequence evidence for a common evolutionary ancestor. Superfamilies are sub-classified into ...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Pethica RB,Levitt M,Gough J

    更新日期:2012-10-18 00:00:00

  • A comprehensive update of the sequence and structure classification of kinases.

    abstract:BACKGROUND:A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. RESULTS:The new survey found the total number of kinase seq...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Cheek S,Ginalski K,Zhang H,Grishin NV

    更新日期:2005-03-16 00:00:00

  • The host-pathogen interaction of human cyclophilin A and HIV-1 Vpr requires specific N-terminal and novel C-terminal domains.

    abstract:BACKGROUND:Cyclophilin A (CypA) represents a potential key molecule in future antiretroviral therapy since inhibition of CypA suppresses human immunodeficiency virus type 1 (HIV-1) replication. CypA interacts with the virus proteins Capsid (CA) and Vpr, however, the mechanism through which CypA influences HIV-1 infecti...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Solbak SM,Wray V,Horvli O,Raae AJ,Flydal MI,Henklein P,Henklein P,Nimtz M,Schubert U,Fossen T

    更新日期:2011-12-20 00:00:00

  • Analysis of the role of PCNA-DNA contacts during clamp loading.

    abstract:BACKGROUND:Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA) in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for DNA polymerases. In an ATP-dependent reaction, clamp loader complexes, such as the Replication Fact...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: McNally R,Bowman GD,Goedken ER,O'Donnell M,Kuriyan J

    更新日期:2010-01-30 00:00:00

  • Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.

    abstract:BACKGROUND:Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. Leptospira interrogans is a spirocha...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Nascimento AS,Catalano-Dupuy DL,Bernardes A,Neto Mde O,Santos MA,Ceccarelli EA,Polikarpov I

    更新日期:2007-10-24 00:00:00

  • The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them.

    abstract:BACKGROUND:Microsomal CYP2E1 metabolizes about 160 hydrophobic exogens, many of which are environmental pollutants. While metabolising xenobiotics CYP2E1 on one hand facilitates in their excretion and on the other hand activates them into the cytotoxins, which may damage the cell. Thus the CYP2E1 activity level signifi...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Kitam VO,Maksymchuk OV,Chashchyn MO

    更新日期:2012-12-17 00:00:00

  • Differential molecular information of maurotoxin peptide recognizing IK(Ca) and Kv1.2 channels explored by computational simulation.

    abstract:BACKGROUND:Scorpion toxins are invaluable tools for ion channel research and are potential drugs for human channelopathies. However, it is still an open task to determine the molecular basis underlying the diverse interactions between toxin peptides and ion channels. The inhibitory peptide Maurotoxin (MTX) recognized t...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Yi H,Qiu S,Wu Y,Li W,Wang B

    更新日期:2011-01-25 00:00:00

  • Analysis of the impact of solvent on contacts prediction in proteins.

    abstract:BACKGROUND:The correlated mutations concept is based on the assumption that interacting protein residues coevolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Approaches based on this concept have been widely used for protein contacts prediction since the 90s. Pr...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Samsonov SA,Teyra J,Anders G,Pisabarro MT

    更新日期:2009-04-15 00:00:00

  • Tripeptide analysis of protein structures.

    abstract:BACKGROUND:An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Anishetty S,Pennathur G,Anishetty R

    更新日期:2002-12-21 00:00:00

  • MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry.

    abstract:BACKGROUND:MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information about stable fragments of multidomain proteins, yield tertiary and quaternary structure data, and hel...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Hennig J,de Vries SJ,Hennig KD,Randles L,Walters KJ,Sunnerhagen M,Bonvin AM

    更新日期:2012-11-15 00:00:00

  • Saturating representation of loop conformational fragments in structure databanks.

    abstract:BACKGROUND:Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Fernandez-Fuentes N,Fiser A

    更新日期:2006-07-04 00:00:00

  • Prediction of protein motions from amino acid sequence and its application to protein-protein interaction.

    abstract:BACKGROUND:Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter in...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Hirose S,Yokota K,Kuroda Y,Wako H,Endo S,Kanai S,Noguchi T

    更新日期:2010-07-13 00:00:00

  • Structural determinant for inducing RORgamma specific inverse agonism triggered by a synthetic benzoxazinone ligand.

    abstract:BACKGROUND:The nuclear hormone receptor RORγ regulates transcriptional genes involved in the production of the pro-inflammatory interleukin IL-17 which has been linked to autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. This transcriptional activity of RORγ is modulat...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Marcotte DJ,Liu Y,Little K,Jones JH,Powell NA,Wildes CP,Silvian LF,Chodaparambil JV

    更新日期:2016-06-01 00:00:00

  • Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II.

    abstract:BACKGROUND:Down-regulation of plasma membrane receptors via the endocytic pathway involves their monoubiquitylation, transport to endosomal membranes and eventual sorting into multi vesicular bodies (MVB) destined for lysosomal degradation. Successive assemblies of Endosomal Sorting Complexes Required for Transport (ES...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Wernimont AK,Weissenhorn W

    更新日期:2004-12-04 00:00:00

  • Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations.

    abstract:BACKGROUND:How proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the m...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Bernini A,Spiga O,Consonni R,Arosio I,Fusi P,Cirri S,Guagliardi A,Niccolai N

    更新日期:2011-10-21 00:00:00

  • Crystal structure of signal regulatory protein gamma (SIRPγ) in complex with an antibody Fab fragment.

    abstract:BACKGROUND:Signal Regulatory Protein γ (SIRPγ) is a member of a closely related family of three cell surface receptors implicated in modulating immune/inflammatory responses. SIRPγ is expressed on T lymphocytes where it appears to be involved in the integrin-independent adhesion of lymphocytes to antigen-presenting cel...

    journal_title:BMC structural biology

    pub_type: 杂志文章


    authors: Nettleship JE,Ren J,Scott DJ,Rahman N,Hatherley D,Zhao Y,Stuart DI,Barclay AN,Owens RJ

    更新日期:2013-07-04 00:00:00