alpha-Helix-double helix interaction shown in the structure of a protamine-transfer RNA complex and a nucleoprotamine model

Insights into the sperm chromatin and implications for male infertility from a protein perspective

Male germ cells undergo an extreme but fascinating process of chromatin remodeling that begins in the testis during the last phase of spermatogenesis and continues through epididymal sperm maturation. Most of the histones are replaced by small proteins named protamines, whose high basicity leads to a tight genomic compaction. This process is epigenetically regulated at many levels, not only by posttranslational modifications, but also by readers, writers, and erasers, in a context of a highly coordinated postmeiotic gene expression program. Protamines are key proteins for acquiring this highly specialized chromatin conformation, needed for sperm functionality. Interestingly, and contrary to what could be inferred from its very specific DNA-packaging function across protamine-containing species, human sperm chromatin contains a wide spectrum of protamine proteoforms, including truncated and posttranslationally modified proteoforms. The generation of protamine knock-out models revealed not only chromatin compaction defects, but also collateral sperm alterations contributing to infertile phenotypes, evidencing the importance of sperm chromatin protamination toward the generation of a new individual. The unique features of sperm chromatin have motivated its study, applying from conventional to the most ground-breaking techniques to disentangle its peculiarities and the cellular mechanisms governing its successful conferment, especially relevant from the protein point of view due to the important epigenetic role of sperm nuclear proteins. Gathering and contextualizing the most striking discoveries will provide a global understanding of the importance and complexity of achieving a proper chromatin compaction and exploring its implications on postfertilization events and beyond. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.

The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria

Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.

The Progress and Promise of RNA Medicine─An Arsenal of Targeted Treatments

In the past decade, there has been a shift in research, clinical development, and commercial activity to exploit the many physiological roles of RNA for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA has catapulted to the forefront of drug research. With diverse functions beyond the role of mRNA in producing antigens or therapeutic proteins, many classes of RNA serve regulatory roles in cells and tissues. These RNAs have potential as new therapeutics, with RNA itself serving as either a drug or a target. Here, based on the CAS Content Collection, we provide a landscape view of the current state and outline trends in RNA research in medicine across time, geography, therapeutic pipelines, chemical modifications, and delivery mechanisms.

Protamine-Based Strategies for RNA Transfection

Protamine is a natural cationic peptide mixture mostly known as a drug for the neutralization of heparin and as a compound in formulations of slow-release insulin. Protamine is also used for cellular delivery of nucleic acids due to opposite charge-driven coupling. This year marks 60 years since the first use of Protamine as a transfection enhancement agent. Since then, Protamine has been broadly used as a stabilization agent for RNA delivery. It has also been involved in several compositions for RNA-based vaccinations in clinical development. Protamine stabilization of RNA shows double functionality: it not only protects RNA from degradation within biological systems, but also enhances penetration into cells. A Protamine-based RNA delivery system is a flexible and versatile platform that can be adjusted according to therapeutic goals: fused with targeting antibodies for precise delivery, digested into a cell penetrating peptide for better transfection efficiency or not-covalently mixed with functional polymers. This manuscript gives an overview of the strategies employed in protamine-based RNA delivery, including the optimization of the nucleic acid's stability and translational efficiency, as well as the regulation of its immunostimulatory properties from early studies to recent developments.

Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding

Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet. The resulting inversion symmetries in aaRS structural biology would have stabilized the initial and subsequent differentiation of coding specificities, rapidly promoting diversity in the proteome. Second, amino acid physical chemistry maps onto tRNA identity elements, establishing reflexive, nanoenvironmental sensing in protein aaRS. Bootstrapping of increasingly detailed coding is thus intrinsic to polypeptide aaRS, but impossible in an RNA world. These notions underline the following concepts that contradict gradual replacement of ribozymal aaRS by polypeptide aaRS: 1) aaRS enzymes must be interdependent; 2) reflexivity intrinsic to polypeptide aaRS production dynamics promotes bootstrapping; 3) takeover of RNA-catalyzed aminoacylation by enzymes will necessarily degrade specificity; and 4) the Central Dogma's emergence is most probable when replication and translation error rates remain comparable. These characteristics are necessary and sufficient for the essentially de novo emergence of a coupled gene-replicase-translatase system of genetic coding that would have continuously preserved the functional meaning of genetically encoded protein genes whose phylogenetic relationships match those observed today.

Condensation of plasmid DNA enhances mitochondrial association in skeletal muscle following hydrodynamic limb vein injection

Mitochondrial gene therapy and diagnosis have the potential to provide substantial medical benefits. However, the utility of this approach has not yet been realized because the technology available for mitochondrial gene delivery continues to be a bottleneck. We previously reported on mitochondrial gene delivery in skeletal muscle using hydrodynamic limb vein (HLV) injection. HLV injection, a useful method for nuclear transgene expression, involves the rapid injection of a large volume of naked plasmid DNA (pDNA). Moreover, the use of a condensed form of pDNA enhances the nuclear transgene expression by the HLV injection. The purpose of this study was to compare naked pDNA and condensed pDNA for mitochondrial association in skeletal muscle, when used in conjunction with HLV injection. PCR analysis showed that the use of condensed pDNA rather than naked pDNA resulted in a more effective mitochondrial association with pDNA, suggesting that the physicochemical state of pDNA plays a key role. Moreover, no mitochondrial toxicities in skeletal muscle following the HLV injection of condensed pDNA were confirmed, as evidenced by cytochrome c oxidase activity and mitochondrial membrane potential. These findings have the potential to contribute to the development for in vivo mitochondrial gene delivery system.

The manner in which DNA is packaged with TFAM has an impact on transcription activation and inhibition

For successful mitochondrial transgene expression, an optimal packaging exogenous DNA is an important issue. We report herein on the effects of DNA packaged with mitochondrial transcription factor A (TFAM), which packages mitochondrial DNA (mtDNA), on the transcription process. Our initial findings indicated that the transcription of the TFAM/DNA complex was activated, when the complex was formed at an optimal ratio. We also found that TFAM has a significant advantage over protamine, a nuclear DNA packaging protein, from the viewpoint of transcription efficiency. This result indicates that TFAM can be useful packaging protein for exogenous DNA to achieve mitochondrial transgene expression.

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.

Transfection efficiency and intracellular fate of polycation liposomes combined with protamine

Endosomal escape and nuclear entry are the two main barriers for successful non-viral gene delivery. To overcome these barriers, polyethylenimine (PEI) with a molecular weight of 800, conjugated to cholesterol (PEI 800-Chol) was synthesized to prepare polycation liposomes (PCLs). The effect of cationic polymers on transfection was investigated by pre-condensing DNA with these before using PCLs. The complexes of PCLs and protamine/DNA nanoparticles (PLPD) were introduced as efficient gene transfer vectors, and displayed obviously higher transfection efficiency (approximately 39-fold) than PCLs/DNA complexes. Kinetics of transgene expression indicated PLPD complexes could be maintained at a relatively high level over 72 h. The order of protamine addition affected the transfection of PLPD complexes. Pre-mixed and post-mixed PLPD complexes improved transfection, although the former was preferred. Distribution of FAM-labeled oligonucleotides (FAM-ODN) in cells mediated by PCLs were throughout the whole cell, while most FAM-ODN were nuclear when transfected with PLPD. These results suggest that the protonation of PEI and membrane destabilization of 1, 2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) increases the endosomal escape ability of vectors. The addition of protamine, containing nuclear localization signals, improved nuclear entry of DNA. The internalization pathways for PCLs involved multiple processes and were possibly dependent on cell lines.

Characterization and performance of nucleic acid nanoparticles combined with protamine and gold

Macromolecular nucleic acids such as DNA vaccines, siRNA, and splice-site switching oligomers (SSO) have vast chemotherapeutic potential. Nanoparticulate biomaterials hold promise for DNA and RNA delivery when a means for binding is identified that retains structure-function and provides stabilization by the nanoparticles. In order to provide these benefits of binding, we combined DNA and RNA with protamine-demonstrating association to gold microparticles by electrophoretic, gel shot, fluorescence, and dynamic laser light spectroscopy (DLLS). A pivotal finding in these studies is that the Au-protamine-DNA conjugates greatly stabilize the DNA; and DNA structure and vaccine activity are maintained even after exposure to physical, chemical, and temperature-accelerated degradation. Specifically, protamine formed nanoparticles when complexed to RNA. These complexes could be detected by gel shift and were probed by high throughput absorbance difference spectroscopy (HTADS). Biological activity of these RNA nanoparticles (RNPs) was demonstrated also by a human tumor cell splice-site switching assay and by siRNA delivery against B-Raf-a key cancer target. Finally, RNA:protamine particles inhibited growth of cultured human tumor cells and bacteria. These data provide new insights into DNA and RNA nanoparticles and prospects for their delivery and chemotherapeutic activity.

Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations

The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.

Progress in developing cationic vectors for non-viral systemic gene therapy against cancer

Initially, gene therapy was viewed as an approach for treating hereditary diseases, but its potential role in the treatment of acquired diseases such as cancer is now widely recognized. The understanding of the molecular mechanisms involved in cancer and the development of nucleic acid delivery systems are two concepts that have led to this development. Systemic gene delivery systems are needed for therapeutic application to cells inaccessible by percutaneous injection and for multi-located tumor sites, i.e. metastases. Non-viral vectors based on the use of cationic lipids or polymers appear to have promising potential, given the problems of safety encountered with viral vectors. Using these non-viral vectors, the current challenge is to obtain a similarly effective transfection to viral ones. Based on the advantages and disadvantages of existing vectors and on the hurdles encountered with these carriers, the aim of this review is to describe the "perfect vector" for systemic gene therapy against cancer.

Dynamic alpha-helices: conformations that do not conform

Structural transitions are important for the stability and function of proteins, but these phenomena are poorly understood. An extensive analysis of Protein Data Bank entries reveals 103 regions in proteins with a tendency to transform from helical to nonhelical conformation and vice versa. We find that these dynamic helices, unlike other helices, are depleted in hydrophobic residues. Furthermore, the dynamic helices have higher surface accessibility and conformational mobility (P-value = 3.35e-07) than the rigid helices. Contact analyses show that these transitions result from protein-ligand, protein-nucleic acid, and crystal-contacts. The immediate structural environment differs quantitatively (P-value = 0.003) as well as qualitatively in the two alternate conformations. Often, dynamic helix experiences more contacts in its helical conformation than in the nonhelical counterpart (P-value = 0.001). There is differential preference for the type of short contacts observed in two conformational states. We also demonstrate that the regions in protein that can undergo such large conformational transitions can be predicted with a reasonable accuracy using logistic regression model of supervised learning. Our findings have implications in understanding the molecular basis of structural transitions that are coupled with binding and are important for the function and stability of the protein. Based on our observations, we propose that several functionally relevant regions on the protein surface can switch over their conformation from coil to helix and vice-versa, to regulate the recognition and binding of their partner and hence these may work as "molecular switches" in the proteins to regulate certain biological process. Our results supports the idea that protein structure-function paradigm should transform from static to a highly dynamic one.

Mammalian sperm chromatin structure and assessment of DNA fragmentation

This review article illustrates the biology of mammalian sperm chromatin structure. The possible causes of DNA (deoxyribonucleic acid) fragmentation are discussed. Also available molecular techniques for assessment of mammalian sperm DNA damage are described.

Per(6-guanidino-6-deoxy)cyclodextrins: synthesis, characterisation and binding behaviour toward selected small molecules and DNA

Per(6-guanidino-6-deoxy)-cyclodextrins , and are novel derivatives, resulting from homogeneous introduction of the guanidino group at the primary side of alpha-, beta- and gamma-cyclodextrins. The products were obtained from the corresponding amino derivatives, as direct guanidinylation of the known bromo-cyclodextrins provided mixtures. The new compounds were fully characterized by NMR spectroscopy and other analytical methods, and their interaction with guest molecules was studied. Strong complexation with 4-nitrophenyl phosphate () disodium salt was observed (K(binding) approximately 5 x 10(4) M(-1)), whereas the non-phosphorylated substrate nitrobenzene () formed a very weak complex. 2D ROESY spectra revealed cavity inclusion in both cases, however the orientation of was opposite to that of , such that the phosphate group is oriented toward the primary side facing the guanidine groups. The strong affinity of towards the phosphorylated guest suggested that interaction with DNA was possible. The new compounds were found to completely inhibit the migration of ultra pure calf thymus DNA during agarose gel electrophoresis, whereas no effects were observed with guanidine alone or with the plain cyclodextrins. Further, the condensation of DNA into nanoparticles in the presence of was demonstrated by atomic force microscopy, confirming strong electrostatic interaction between the biopolymer and the multicationic products . The strong guanidine-phosphate interactions between and DNA were therefore attributed to the clustering of the guanidine groups in the primary area of the cyclodextrin. Cavity effects could not be assessed.

Electrophoretic analysis of proteins and enantiomers using capillaries modified by a successive multiple ionic-polymer layer (SMIL) coating technique

The applicability of three-layer coatings consisting of three different polymers (A(+)-B(-)-C(+) coating) prepared by a successive multiple ionic-polymer layer (SMIL) coating technique to the immobilization of polypeptides and/or proteins onto the inner surface of the capillaries was investigated to provide a high-performance separation medium for proteins and enantiomers in capillary electrophoresis (CE). To obtain a stable protein-coated capillary, high molecular mass poly(ethyleneimine) (PEI) was employed as the first layer in the A(+)-B(-)-C(+) coating, and then a cationic protein was immobilized as the third layer. Comparisons of analytical performances between the A(+)-B(-)-C(+) coating and the conventional SMIL-coated (A(+)-B(-)-A(+) coating) capillary were conducted. The CE separation of cationic proteins was successfully achieved with the prepared capillaries. In addition, the polypeptide- and protein-coated capillaries were applied to the chiral separation of a binaphthyl compound. It should be noted that the chiral separation efficiency was strongly dependent on the second anionic polymer layer of the coating. Effects of the interaction between oppositely charged ionic polymer layers on the separation efficiency are discussed.

Cationic compounds used in lipoplexes and polyplexes for gene delivery

Gene transfer represents an important advance in the treatment of both genetic and acquired diseases. Many cationic lipids and cationic polymers naturally occurred or synthesized have been used for gene transfer. They have the advantages over viral gene transfer as non-immunogenic, easy to produce and not oncogenic. These cationic compounds, however, have the major limitations of inefficient transfection and toxicity to cells. For overcoming these problems, many new cationic compounds were developed since the first cationic lipid, DOTMA, was found usage in gene therapy. This article reviews cationic lipids for gene therapy from chemistry viewpoint and we classify these compounds as monovalent cationic lipids, polyvalent cationic lipids, cationic polymers, guanidine containing compounds, cationic peptides and cholesterol containing compounds, and hope to provide suggestions on the development of this variety of cationic compounds through the discussion.

Generation of CTL responses using Kunjin replicon RNA

The Kunjin replicon was used to express a polytope that consisted of seven hepatitis C virus cytotoxic T lymphocyte epitopes and one influenza cytotoxic T lymphocyte epitope for vaccination studies. The self-replicating nature of, and expression from, the ribonucleic acid was confirmed in vitro. Initial vaccinations with one dose of Kun-Poly ribonucleic acid showed that an influenza-specific cytotoxic T lymphocyte response was elicited more efficiently by intradermal inoculation compared with intramuscular delivery. Two micrograms of ribonucleic acid delivered in the ear pinnae of mice was sufficient to elicit a detectable cytotoxic T lymphocyte response 10 days post-vaccination. Further vaccination studies showed that four of the seven hepatitis C virus cytotoxic T lymphocyte epitopes were able to elicit weak cytotoxic T lymphocyte responses whereas the influenza epitope was able to elicit strong, specific cytotoxic T lymphocyte responses following three doses of Kun-Poly ribonucleic acid. These studies vindicate the use of the Kunjin replicon as a vector to deliver encoded proteins for the development of cell-mediated immune responses.

Development of non-viral vectors for systemic gene delivery

One of the major challenges for gene therapy is systemic delivery of a nucleic acid directly into an affected tissue. This requires developing a vehicle which is able to protect the nucleic acid from degradation, while delivering the gene of interest to the specific tissue and specific subcellular compartment. In this review, we summarize some of the recent advances in new non-viral delivery systems for systemic administration. Two types of gene delivery systems are described: (i) LPD1 (cationic liposome-entrapped, polycation-condensed DNA, type 1), and (ii) retention-time mediated naked DNA delivery. Hypothesized mechanisms for these systemic gene transfers are also discussed.

What does it mean to be natively unfolded?

Natively unfolded or intrinsically unstructured proteins constitute a unique group of the protein kingdom. The evolutionary persistence of such proteins represents strong evidence in the favor of their importance and raises intriguing questions about the role of protein disorders in biological processes. Additionally, natively unfolded proteins, with their lack of ordered structure, represent attractive targets for the biophysical studies of the unfolded polypeptide chain under physiological conditions in vitro. The goal of this study was to summarize the structural information on natively unfolded proteins in order to evaluate their major conformational characteristics. It appeared that natively unfolded proteins are characterized by low overall hydrophobicity and large net charge. They possess hydrodynamic properties typical of random coils in poor solvent, or premolten globule conformation. These proteins show a low level of ordered secondary structure and no tightly packed core. They are very flexible, but may adopt relatively rigid conformations in the presence of natural ligands. Finally, in comparison with the globular proteins, natively unfolded polypeptides possess 'turn out' responses to changes in the environment, as their structural complexities increase at high temperature or at extreme pH.

3PO, a novel nonviral gene delivery system using engineered Ad5 penton proteins

This study describes the development of 3PO, a nonviral, protein-based gene delivery vector which utilizes the highly evolved cell-binding, cell-entry and intracellular transport functions of the adenovirus serotype 5 (Ad5) capsid penton protein. A penton fusion protein containing a polylysine sequence was produced by recombinant methods and tested for gene delivery capability. As the protein itself is known to bind integrins through a conserved consensus motif, the penton inherently possesses the ability to bind and enter cells through receptor-mediated internalization. The ability to lyse the cellular endosome encapsulating internalized receptors is also attributed to the penton. The recombinant protein gains the additional function of DNA binding and transport with the appendage of a polylysine motif. This protein retains the ability to form pentamers and mediates delivery of a reporter gene to cultured cells. Interference by oligopeptides bearing the integrin binding motif suggests that delivery is mediated specifically through integrin receptor binding and internalization. The addition of protamine to penton-DNA complexes allows gene delivery in the presence of serum.

Signal peptides bind and aggregate RNA. An alternative explanation for GTPase inhibition in the signal recognition particle

N-terminal signal sequences can direct nascent protein chains to the inner membrane of prokaryotes and the endoplasmic reticulum of eukaryotes by interacting with the signal recognition particle. In this study, we show that isolated peptides corresponding to several bacterial signal sequences inhibit the GTPase activity of the Escherichia coli signal recognition particle, as previously reported (Miller, J. D., Bernstein, H. D., and Walter, P. (1994) Nature 367, 657-659), but not by the direct mechanism proposed. Instead, isolated signal peptides bind nonspecifically to the RNA component and aggregate the entire signal recognition particle, leading to a loss of its intrinsic GTPase activity. Surprisingly, only "functional" peptide sequences aggregate RNA; the peptides in general use as "nonfunctional" negative controls (e.g. those with deletions or charged substitutions within the hydrophobic core), are sufficiently different in physical character that they do not aggregate RNA and thus have no effect on the GTPase activity of the signal recognition particle. We propose that the reported effect of functional signal peptides on the GTPase activity of the signal recognition particle is an artifact of the high peptide concentrations and low salt conditions used in these in vitro studies and that signal sequences at the N terminus of nascent chains in vivo do not exhibit this activity.

Sequence complexity of disordered protein

Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins.

Why are "natively unfolded" proteins unstructured under physiologic conditions?

"Natively unfolded" proteins occupy a unique niche within the protein kingdom in that they lack ordered structure under conditions of neutral pH in vitro. Analysis of amino acid sequences, based on the normalized net charge and mean hydrophobicity, has been applied to two sets of proteins: small globular folded proteins and "natively unfolded" ones. The results show that "natively unfolded" proteins are specifically localized within a unique region of charge-hydrophobicity phase space and indicate that a combination of low overall hydrophobicity and large net charge represent a unique structural feature of "natively unfolded" proteins.

Are there molecules of nucleoprotamine?

A short critical review of the data related to protamine and nucleoprotamine (DNP) structure is given. A new model is proposed for DNP structure in which protamine molecules are located in channels between the DNA molecules. DNA molecules are arranged hexagonally in the x-y plane, whereas their relative positions with respect to the z-axis are shifted by 0, 1/3, and 2/3 of the pitch of the double helix. As a result, large cavities are formed in three out of six channels surrounding each DNA molecule where the large grooves are juxtaposed. Protamine molecules are also proposed to have some secondary/tertiary structure prior to complex formation. Inside the channels, a protamine molecule modifies its shape to fill the large grooves of all of the three surrounding DNA molecules simultaneously, and might possibly be in touch with other protamine molecules in neighbouring positions as well. This disposition allows the protamine molecules to be located between DNA molecules without a significant increase in the lattice parameters.

Analysis of DNA-protamine interactions by optical detection of magnetic resonance

Optically detected magnetic resonance (ODMR) has been used to identify the binding site of a synthetic protamine subdomain to the major groove of DNA. A 14 amino acid peptide (R6WGR6) analog of the central DNA binding domain of bull protamine was synthesized with phenylalanine replaced by tryptophan (Trp). The peptide was bound to double-stranded poly(dABrdU) and to calf thymus DNA (CT DNA) and the complexes characterized as "wet" solids using ODMR techniques. The appearance of the D + E transition in the slow passage ODMR and of short-lived components in the phosphorescence decay of the complex of R6WGR6 with poly(dABrdU) is diagnostic of a heavy atom effect. This can only occur if the peptide binds in the major groove of poly(dABrdU). The microenvironment of Trp in the nucleoprotein complex was characterized by phosphorescence, radiative decay lifetimes, and low-temperature ODMR measurements before and after binding to DNA. Bathochromic shifts in the phosphorescence emission upon exciting to the red in CT DNA-peptide suggest that the Trp is in a polar environment, while the red-shifted position of the 0, 0-band emission points to a more polarizable environment. The heavy atom effect strongly suggests a Trp location within the major groove of DNA. A partial stacking of Trp with the polarizable nucleobases and simultaneous interactions with the phosphate-guanidinium ion pairs and/or water molecules in the major groove of DNA which might not be totally displaced upon binding of the peptide could explain this conflicting evidence. Extrapolation of results from the system studied to protamine binding in sperm chromatin strongly suggests that the predominant binding site of protamine is the major groove of DNA.

Mediation of oxidative DNA damage by nickel(II) and copper(II) complexes with the N-terminal sequence of human protamine HP2

The potential of Ni(II) and Cu(II) complexes with Arg-Thr-His-Gly-Gln-Ser-His-Tyr-Arg-Arg-Arg-His-Cys-Ser-Arg-amide (HP2(1-15)), a peptide modeling the N-terminal amino acid sequence of human protamine HP2, to mediate oxidative DNA damage was studied by measurements of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) generation from 2'-deoxyguanosine (dG) and calf thymus DNA and by formation of double-strand breaks in calf thymus DNA. The concentrations of reagents were 0.1 mM dG and the metal-HP2(1-15) complex, 1 mM H2O2, 1.5 mM DNA (per phosphate group), 100 mM phosphate buffer, pH 7.4, ambient O2. Samples were incubated at 37 degrees C for 16-24 h. The Cu(II)-HP2(1-15) complex was found to be an effective promoter of the formation of 8-oxo-dG from both dG and DNA with ambient O2 (approximately 13- and 3-fold increase versus the oxidant alone, respectively) and H2O2 (approximately 25-fold increase in either case). The Ni(II)-HP2(1-15) complex was ineffective with O2 versus 8-oxo-dG production from both substrates but markedly enhanced the attack of H2O2 on dG and DNA (approximately 5-fold increase of 8-oxo-dG production in either case). Both Cu(II)- and Ni(II)-HP2(1-15) equally promoted double-strand scission by H2O2 in calf thymus DNA. The promotion by the complexes of dG and DNA oxidation with H2O2 was accompanied by oxidative damage to the complexes themselves, consisting of decreasing contents of their His (to approximately 50% of control in either complex) and especially Tyr (down to 48% of control in Cu(II)- and 19% in Ni(II)-HP2[1-15]) residues, as well as appearance of aspartic acid, the known oxidation product of His residues in peptides (up to 22% vs Gly for Cu(II)- and 10% for Ni(II)-HP2(1-15)). The above results provide a novel chemical mechanism of Cu(II) and Ni(II) toxicity and may have wide implications for reproductive and transgenerational effects of metal exposure.

Evidence of novel secondary structure in DNA-bound protamine is revealed by Raman spectroscopy

Raman spectroscopy studies of protamine-DNA complexes are reported for samples in the solid state at 98% relative humidity. Previous reports utilizing other physical techniques have indicated the presence of B-form DNA in protamine-DNA complexes. The present Raman data support the assignment of a modified B-form which is characterized by appreciable unstacking of the bases. The quality of the present spectra has made it possible, for the first time, to obtain the Raman spectrum of DNA-bound protamine by digital spectral subtraction. The difference spectrum indicates that protamine adopts an unusual secondary structure upon binding to DNA. A dominant amide I band is observed at 1683 cm-1 which is indicative of neither an alpha-helix or beta-sheet conformation. An amide I band at this position has been associated with the 1-->3 hydrogen bond that occurs within a gamma-turn [Bandekar, J., & Krimm, S. (1985) Int. J. Pept. Protein Res. 26, 158-165]. On the basis of this assignment, as well as preliminary results obtained by computer modeling, we propose a new model for the secondary structure of DNA-bound protamine that is rich in 1-->3 hydrogen bonding. Spectral data demonstrate that this structure is absent in protamine molecules in solution. Analyses of spectra of polyarginine-DNA complexes suggest that polyarginine, although similar to protamine in primary structure, assumes a conformation when bound to DNA that is distinct from that adopted by protamine.

Interaction of mammalian sperm nuclear protamines and peptides derived thereof with immobilized zinc

The interaction of mammalian and human protamines with zinc was studied by immobilized metal ion affinity chromatography (IMAC). The affinity of protamines containing blocked cysteine residues was found to correlate in part with the presence and number of histidine residues in the protamine structure: absence or low affinity of P1 protamines containing 0 or 1 histidine residue; high affinity of human P2 protamine containing 9 histidines. Nevertheless a fraction strongly retained on an IDA-Zn(II) column was observed for P1 protamines with one histidine in the N-terminal sequence (ram and boar protamines). The strong binding was found to be related to the presence of tyrosine, serine and threonine closely spaced to the histidyl side chain. In the case of human protamine P2, the strong retention on the IDA-Zn(II) column seems to result from the additive contribution of all the histidine residues of the molecule. Thus, strong retention of protamines in IMAC seems to depend on an additive contribution of amino-acid side chains: histidine, tyrosine, serine, threonine and perhaps arginine. The high affinity of protamines, more especially P2 protamines, for zinc suggests that this metal ion could play a role for their correct folding and binding to DNA.

Helical structure of basic proteins from spermatozoa. Comparison with model peptides

We describe structural studies carried out with some basic proteins found in association with DNA in the spermatozoa of molluscs and echinoderms. We have studied proteins related to histone H1 as well as protamines. Structural prediction methods show that these proteins have a strong helical potential and contain several turns, mainly of the SPKK type. No beta structures were found. Strong structural similarities have been detected between distantly related species. The presence of helical regions is confirmed by circular dichroism in trifluoroethanol solution. The influence of the SPKK turns is also evident in the CD spectra. In proteins which contain a high percentage of arginine we conclude that conventional prediction methods should be modified in order to allow for a higher helical potential for this amino acid residue. Synthetic peptides with a sequence present in the C-terminal region of histone H1 have also been studied. It was found that octapeptides may only acquire a small amount of structure, whereas hexadecapeptides are 50-60% helical. These studies strongly suggest that both protamines and proteins related to the C-terminal part of histone H1 interact with DNA mainly in the alpha-helical conformation.

Structure and function of protamines: an 1H nuclear magnetic resonance investigation of the interaction of clupeines with mononucleotides

Protamines form a class of low-molecular-weight proteins that protect the chromosomal DNA in the spermatic cells of eukaryotic organisms. Protamines are located in the small and/or large groove of DNA where they complex the DNA nucleotides. Very little is known up to date on the role and specificity of binding of the various protamine fractions belonging to a single eukaryotic species. In the present paper, a detailed investigation on the complexation properties of the protamine fractions (clupeines) extracted from herrings has been carried out by means of proton nuclear magnetic resonance and ultraviolet absorbtion data. In particular, the binding properties of the clupeine fractions with purinic (5'dAMP) and pyrimidinic (5'dCMP) mononucleotides have been measured and analysed at different clupeine concentrations. The results indicate that, contrary to previous preliminary hypothesis, the three clupeine fractions exhibit quite comparable binding properties toward mononucleotides. In addition it has been found that nucleotides can induce a conformational transition of the disorder-order type in the clupeine molecules and this property is concentration and temperature dependent. It is concluded that, as far as specificity is concerned, the clupeine fractions seem to possess the same behaviour toward mononucleotides.

Studies on the function mechanism of a Formosan grey mullet protamine-mugiline beta M6: interaction of the M6 and M6 fragments with DNA

The interaction of three peptide segments of one component of Formosan grey mullet protamine (mugiline beta M6), obtained by chemical and enzymatic cleavage, with DNA was studied by spectroscopic measurement, thermal denaturation and circular dichroism. The data obtained were then compared with those of whole M6 and other fish protamines such as salmine of salmon and clupeine of herring. M6-B-I, which lacks C-terminal 11 amino acids in M6, showed significantly different properties. It showed remarkably high DNA aggregating ability which was due to a conformational change of DNA from B to A form. The conformational change of DNA induced by the binding of M6-B-I was reproduced by the carboxypeptidase B digestion of DNA-M6 complex. From these results, the arginine-rich, C-terminal domain of the M6 molecule was estimated to be essential for natural DNA binding.

Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin

We have used indirect immunofluorescence of polytene chromosomes to examine the chromatin distribution of a 52-kD Drosophila protein designated B52. B52 is localized to transcriptionally active loci and, at the highly decondensed heat shock loci, can be seen to bracket the RNA polymerase II fluorescence signals symmetrically. We have also examined the distribution of B52 on nonpolytene chromosomes in Drosophila cell cultures with an in vivo UV cross-linking method and find that, here too, B52 is associated with boundaries of transcriptionally active chromatin. The predicted primary amino acid sequence of B52 reveals two regions with similarities to a number of other proteins known to interact with nucleic acids.

The number of positively charged amino acids in the basic domain of Tat is critical for trans-activation and complex formation with TAR RNA

The basic domain of Tat is required for trans-activation of viral gene expression. We have performed scanning peptide studies to demonstrate that only this domain is capable of binding to the TAR RNA stem-loop. Strikingly, the basic domain of the other human immunodeficiency virus trans-acting factor, Rev, but no other region, is also capable of binding to TAR. Peptide derivatives of Tat do not require the highly conserved glutamine residue at position 54 for TAR binding, since it may be substituted or deleted. In addition, the two lysine residues may be replaced by arginines. Analysis of binding and trans-activation demonstrated that homopolymers of arginine can completely substitute for the basic domain. Such homopolymers have high affinity for wild-type TAR RNA and lower affinity for mutant TAR. Homopolymers of six to nine arginines substituting for the basic domain of Tat enable full trans-activation in vivo. Homopolymers of at least seven arginines are required for detectable in vitro complex formation, although approximately 30% trans-activation is achieved with a mutant Tat containing only five arginines.

Primary structure of toad sperm protamines and nucleotide sequence of their cDNAs

Acid extract of mature sperm of the toad, Bufo japonicus, exclusively comprised sperm-specific basic proteins which moved faster than somatic histones on acid/urea/Triton X-100 polyacrylamide gel electrophoresis. When these proteins were purified by reversed-phase high-performance liquid chromatography they were found to consist of three components; one of these was a phosphorylated form of another, so that there were only two distinct components (P1 and P2). Amino acid sequence analyses indicated that the components both contained 39 amino acid residues, with 43.6% Arg, and differed only in the 28th amino acid residue (P1, Asp; P2, Glu). They had molecular masses of 5092 Da (P1) and 5106 Da (P2). The nucleotide sequences of cDNA clones encoding P1 (245 bases) and P2 (305 bases) showed that the difference in the amino acid residue between P1 and P2 was due to the difference of a nucleotide at position +87. Both cDNAs possessed a canonical signal (AATAAA) for polyadenylation and/or cleavage of transcript at the 3' untranslational region. Statistical analyses of amino acid sequence similarities suggested that the Bufo protamines are homologous with the protamines of fishes rather than with those of avian/mammalians.