Role Of Protein Binding Research Articles

TMT-based quantitative proteomics reveals the effects of electromagnetic field and freezing preservation techniques on mutton quality

This study investigated the effects of electromagnetic field preservation (EP) and freezing storage (FS) on the quality of northern Qianbei Ma mutton. Using tandem mass tagging (TMT)-labeled quantitative proteomics and bioinformatics, it was observed that EP more effectively inhibited pH increase and maintained a* and b* values compared to FS. Furthermore, the EP group was able to better maintain the water-holding capacity and tenderness of the mutton under prolonged storage. Proteomics analysis identified 397 differentially expressed proteins (DEPs) between the two storage methods at the same storage duration. GO and KEGG enrichment analyses indicated that proteins such as A0A452DSW4, A0A452E8M7, and D3JYV6 were involved in energy metabolism and redox processes, while A0A452EJ66, A0A452DSW4, and A0A452FJE8 played significant roles in protein binding. Overall, EP technology demonstrated superior benefits for maintaining mutton quality, suggesting a novel approach for mutton preservation.

Underestimation of tetracycline antibiotic residues in chicken meat: The role of protein binding

Interesting variations in the analyte content were observed in chicken samples contaminated with tetracycline antibiotics (TCs) following pretreatment with various enzymatic hydrolysis before quantification by conventional analytical methods. Compared with untreated samples, the detectable contents of three TCs in protease-treated samples were 1.51 to 2.05 times higher, whereas lipase treatment did not significantly influence the contents. The marked changes following protease treatment confirmed the presence of protein-associated antibiotics. Infrared spectroscopy analysis indicated that the formation of protein-bound antibiotics resulted from non-covalent interactions between TCs and proteins. Further dissociation experiments determined that the intermolecular forces involved hydrogen bonding, hydrophobic interactions, and electrostatic attraction. Molecular docking substantiated these forces and detailed the binding mechanism at the molecular level. Moreover, the masking effect of protein binding on the determination of TCs was also evidenced in an additional 30 positive chicken samples, suggesting that the actual residue levels of TCs in protein-rich foodstuffs are underestimated.

Downregulation of LAMB3 Altered the Carcinogenic Properties of Human Papillomavirus 16-Positive Cervical Cancer Cells.

Nearly all cervical cancer cases are caused by infection with high-risk human papillomavirus (HR-HPV) types. The mechanism of cervical cell transformation is related to the powerful action of viral oncoproteins and cellular gene alterations. Transcriptomic data from cervical cancer and normal cervical cells were utilized to identify upregulated genes and their associated pathways. The laminin subunit beta-3 (LAMB3) mRNAwas overexpressed in cervical cancer and was chosen for functional analysis. The LAMB3 was predominantly expressed in the extracellular region and the plasma membrane, which play a role in protein binding and cell adhesion molecule binding, leading to cell migration and tissue development. LAMB3 was found to be implicated in the pathway in cancer and the PI3K-AKT signaling pathway. LAMB3 knockdown decreased cell migration, invasion, anchorage-dependent and anchorage-independent cell growth and increased the number of apoptotic cells. These effects were linked to a decrease in protein levels involved in the PI3K-AKT signaling pathway and an increase in p53 protein. This study demonstrated that LAMB3 could promote cervical cancer cell migration, invasion and survival.

Structural Analysis and Protein Binding of Cephalosporins.

Cephalosporins are a widely used subclass of β-lactam antibiotics that demonstrate variable protein binding independent of generation or antibiotic coverage. Prior work analyzed carbon3 (C3) and carbon7 (C7) substituents (locations of R2 and R1 groups respectively) for protein binding interactions. This study builds upon these results with statistical analysis of additional agents of the class. Chemical structures of 23 cephalosporins were used to identify the presence of 40 functional groups, and correlative relationships were identified using established protein binding data. Four functional groups were significantly correlated with protein binding: tetrazole (positive association), pyridinium, primary amine, and quaternary amine (negative associations). Cephalosporins with a negative charge at physiological pH were associated with increased protein binding. Analysis of tetrazole-containing cephalosporins and ceftriaxone indicates the need for further study of the potential role in protein binding of neutral or negatively charged aromatic nitrogen heterocycles linked at the C3 position by a thiomethylene group.

Unravelling the orientation of the inositol-biphosphate ring and its dependence on phosphatidylinositol 4,5-bisphosphate cluster formation in model membranes

HypothesisInositol phospholipids are well known to form clusters in the cytoplasmic leaflet of the plasma membrane that are responsible for the interaction and recruitment of proteins involved in key biological processes like endocytosis, ion channel activation and secondary messenger production. Although their phosphorylated inositol ring headgroup plays an important role in protein binding, its orientation with respect to the plane of the membrane and its lateral packing density has not been previously described experimentally. ExperimentsHere, we study phosphatidylinositol 4,5-bisphosphate (PIP2) planar model membranes in the form of Langmuir monolayers by surface pressure-area isotherms, Brewster angle microscopy and neutron reflectometry to elucidate the relation between lateral (in-plane) and perpendicular (out-of-plane) molecular organization of PIP2. FindingsDifferent surface areas were explored through monolayer compression, allowing us to correlate the formation of transient PIP2 clusters with the change in orientation of the inositol-biphosphate headgroup, which was experimentally determined by neutron reflectometry.

Transcriptomic profiling of Paulownia elongata in response to heat stress

Rising global temperatures have caused a substantial loss in crop productivity throughout the world. Understanding the fundamental mechanisms underlying tolerance to heat stress in plants has become increasingly relevant, particularly as global warming continues to rise. The goal of our study was to identify and analyze heat stress-induced transcriptomic changes in Paulownia elongata plants. Paulownia elongata are fast growing trees known for their ability to grow in a wide range of temperatures. However, the genes responsible for its thermotolerance have not yet been identified and studied in detail. In our study, we used RNA-sequencing (RNA-seq) to analyze changes in gene expression at the transcriptomic level after inducing heat stress and identified 4,435 genes as differentially expressed. Most of the genes found to be upregulated play a critical role in protein binding, unfolding, retention, and transport, suggesting that heat tolerance in plants can be achieved by protecting native proteins. The genes and pathways identified in this study can serve as valuable targets in heat tolerance studies and development of heat tolerant plants. To the best of our knowledge, this is the first in-depth report of heat-induced transcriptome analysis in P. elongata.

Comprehensive Analysis of the Expression and Prognosis for DCTPP1 gene in Breast Cancer

Background: Breast cancer is a common malignancy in women. DCTPP1 is a potential target for the development of antitumor drugs, and plays an important role in the process of DNA replication. Aims: To investigate the biological role of DCTPP1 gene, as well as its expression in breast cancer and its relation to patient prognosis. Materials and Methods: Breast cancer data was derived from the TCGA database. Using the UALCAN database, the expression level of DCTPP1 mRNA in breast cancer tissues was investigated. The expression of DCTPP1 in various pathological types of breast cancer was studied using the Human Protein Atlas. UALCAN was also used to investigate the relationship between DCTPP1 gene expression and breast cancer patient prognosis. Bioinformatics studied the proteins related to DCTPP1 expression and their roles in the GeneMANIA and WebGestalt databases. Results: DCTPP1 mRNA was significantly expressed in breast cancer compared to normal breast tissue (P<0.001). DCTPP1 was shown to be highly expressed in breast cancer tissues from different pathological types and stages (P<0.001). The DCTPP1 protein was expressed at a higher frequency in breast cancer than in normal breast tissue. When compared to patients with low DCTPP1 expression, patients with high DCTPP1 expression had a considerably shorter overall survival time. The 20 proteins related to DCTPP1 expression were mostly located in the nucleus and membrane, and were involved in biological regulation, stimulus response, metabolic process, and other processes, according to gene ontology analysis. It plays an important role in protein binding, ion binding, and nucleic acid binding. Conclusion: DCTPP1 is highly expressed in breast cancer, and is associated to a poor prognosis for patients with breast cancer. DCTPP1 may be a potential therapy and intervention target for breast cancer.

Classification and Computational Analysis of Arabidopsis thaliana Sperm Cell-Specific F-Box Protein Gene 3p.AtFBP113.

In plants, F-box proteins (FBPs) constitute one of the largest superfamilies of regulatory proteins. Most F-box proteins are shown to be an integral part of SCF complexes, which carry out the degradation of proteins and regulate diverse important biological processes. Anthers and pollen development have a huge importance in crop breeding. Despite the vast diversity of FBPs in Arabidopsis male reproductive organs, their role in anther and pollen development is not much explored. Moreover, a standard nomenclature for naming FBPs is also lacking. Here, we propose a standard nomenclature for naming the FBPs of Arabidopsis thaliana uniformly and carry out a systematic analysis of sperm cell-specific FBP gene, i.e., 3p.AtFBP113 due to its reported high and preferential expression, for detailed functional annotation. The results revealed that 3p.AtFBP113 is located on the small arm of chromosome and encodes 397 amino acid long soluble, stable, and hydrophilic protein with the possibility of localization in various cellular compartments. The presence of the C-terminal F-box associated domain (FBA) with immunoglobulin-like fold anticipated its role in protein binding. Gene ontology based functional annotation and tissue-specific gene co-expression analysis further strengthened its role in protein binding and ubiquitination. Moreover, various potential post/co-translational modifications were anticipated and the predicted tertiary structure also showed the presence of characteristic domains and fold. Thus, the outcomes of the study will be useful in developing a better understating of the function of 3p.AtFBP113 during the process of pollen development, which will be helpful for targeting the gene for manipulation of male fertility that has immense importance in hybrid breeding.

Targeted exome sequencing identified a novel USH2A mutation in a Chinese usher syndrome family: a case report

BackgroundUsher syndrome is a disease with a heterogeneous phenotype and genotype. Our purpose was to identify the gene mutation in a Chinese family with Usher syndrome type 2 and describe the clinical features.Case presentationA 23-year-old man complained of a 10-year duration of nyctalopia and a 3-year decline in visual acuity of both eyes accompanied by congenital dysaudia. To clarify the diagnosis, the clinical symptoms were observed and analysed in combination with comprehensive ophthalmologic examinations as well as genetic analysis (targeted exome sequencing, TES). A typical clinical presentation of Usher syndrome of the fundus was found, including a waxy yellow-like disc, bone-spicule formations and retinal vessel stenosis. Optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) showed loss of the ellipsoid zone and a reduction in paracaval vessel density in both eyes. Genetic analysis identified a novel homozygous c.8483_8486del (p.Ser2828*) mutation in USH2A. The mutation resulted in premature termination of translation and caused the deletion of 19 fibronectin type 3 domains (FN3), transmembrane (TM) region and PDZ-binding motif domain, which play an important role in protein binding. After combining the clinical manifestations and genetic results, the patient was diagnosed with Usher syndrome type 2.ConclusionWe found a novel c.8483_8486del mutation in the USH2A gene through TES techniques. The results broaden the spectrum of mutations in Usher syndrome type 2 and suggest that a combination of clinical information and molecular diagnosis via TES could help Usher syndrome patients obtain a better diagnosis.

Bone Marrow Stromal Antigen 2 Is Critical for IFNy-Dependent Hematopoietic Stem Cell Activation

Bone marrow failure is a significant complication of many chronic infections, which affect a third of the world's population. The inflammatory cytokine interferon-gamma (IFNy) contributes to bone marrow failure syndromes by activating hematopoietic stem cells (HSCs) and impairing their self-renewal. IFNy upregulation during many chronic infections such as tuberculosis, HIV and hepatitis B directly depletes hematopoietic stem cells (HSCs). The mechanisms by which IFNy drives the loss of quiescence and ultimate exhaustion of HSCs remain poorly understood, but may be related to changes in the interaction between HSCs and the bone marrow (BM) microenvironment, or BM niche. Current evidence suggests that quiescent HSCs reside predominantly in the vascular niche, where the production of stem cell factor (SCF) from endothelial cells and CXCL12 from perivascular CXCL12 abundant reticular (CAR) stromal cells are critical for maintaining their quiescence. The goal of our work was to determine whether IFNy signaling alters HSC interactions within the niche. We performed transcriptomic analysis of IFNy-stimulated HSCs and focused on changes in cell-surface expressed genes that may influence HSC-niche interactions. Our analysis revealed Bone Marrow Stromal Antigen 2 (BST2) as the only surface protein upregulated on HSCs upon 24-hour IFNy stimulation. To study the effects of BST2 on HSC-niche interactions, we performed intravital imaging using two reporter mouse models: CXCL12-GFP reporter mice in which CAR cells are labeled with GFP, and CXCL12-GFP Krt18-Cre LSL-tdTomato dual reporter mice in which CAR cells are labelled with GFP and HSCs are labeled with tdTomato. After exogenously labeling and transferring HSCs into CXCL12-GFP mice or endogenously labeling HSCs in the CXCL12-GFP Krt18-Cre LSL-tdTomato mice, we observed that HSCs stimulated with IFNy were significantly distanced from CAR cells compared to pre-treated controls. These findings are consistent with other reports that chemotherapeutic and inflammatory stress disrupts HSC interactions with the niche and promotes HSC migration. Conversely, we observed no change in HSC distancing from CAR cells after IFNy stimulation of IFNy-receptor deficient HSCs, suggesting that the observed HSC displacement was due to a cell autonomous mechanism. These changes were not due to a loss of CXCL12 receptor (CXCR4) expression or disrupted capacity of HSCs to migrate towards CXCL12. Interestingly, Intravital imaging using BST2-deficient HSCs revealed that BST2 KO HSCs do not re-localize from CAR cells during IFNy stimulation. Increased BST2 expression has been linked to the migration, adhesion and metastasis of various cancer cells and we explored whether it could serve a similar role in protein binding in HSCs. Using in vitro plate binding assays, we found that IFNy-treatment promoted increased HSC binding to E-selectin via BST2, as well as increased HSC homing to the bone marrow, a property that is dependent on E-selectin binding. Finally, to determine whether BST2 affects IFNy-dependent HSC activation we performed cell cycle analysis of WT and BST2 KO HSCs. We discovered that the loss of BST2 protects against HSC activation during Mycobacterium avium infection. Furthermore, HSC depletion during chronic infection was mitigated in BST2 KO mice. Our data identifies BST2 as a key protein that influences niche relocalization and activation in response to inflammatory stimulation. This study expands our understanding of factors that contribute to HSC activation and loss of quiescence. These findings could shed light on novel therapeutic interventions for patients who develop pancytopenia or bone marrow failure due to chronic inflammation. Disclosures No relevant conflicts of interest to declare.

In Silico Modeling of Spirolides and Gymnodimines: Determination of S Configuration at Butenolide Ring Carbon C-4

Only few naturally occurring cyclic imines have been fully structurally elucidated or synthesized to date. The configuration at the C-4 carbon plays a pivotal role in the neurotoxicity of many of these metabolites, for example, gymnodomines (GYMs) and spirolides (SPXs). However, the stereochemistry at this position is not accessible by nuclear Overhauser effect—nuclear magnetic resonance spectroscopy (NOE-NMR) due to unconstrained rotation of the single carbon bond between C-4 and C-5. Consequently, the relative configuration of GYMs and SPXs at C-4 and its role in protein binding remains elusive. Here, we determined the stereochemical configuration at carbon C-4 in the butenolide ring of spirolide- and gymnodimine-phycotoxins by comparison of measured 13C NMR shifts with values obtained in silico using force field, semiempirical and density functional theory methods. This comparison demonstrated that modeled data support S configuration at C-4 for all studied SPXs and GYMs, suggesting a biosynthetically conserved relative configuration at carbon C-4 among these toxins.

Diversity and sequence motifs of the bacterial SecA protein motor

SecA is an essential component of the Sec protein secretion pathway in bacteria. Secretory proteins targeted to the Sec pathway by their N-terminal signal peptide bind to SecA, which couples binding and hydrolysis of adenosine triphosphate with movement of the secretory protein across the membrane-embedded SecYEG protein translocon. The phylogenetic diversity of bacteria raises the important question as to whether the region of SecA where the pre-protein binds has conserved sequence features that might impact the reaction mechanism of SecA. To address this question we established a large data set of SecA protein sequences and implemented a protocol to cluster and analyze these sequences according to features of two of the SecA functional domains, the protein binding domain and the nucleotide-binding domain 1. We identify remarkable sequence diversity of the protein binding domain, but also conserved motifs with potential role in protein binding. The N-terminus of SecA has sequence motifs that could help anchor SecA to the membrane. The overall sequence length and net estimated charge of SecA sequences depend on the organism.

How do Nanoparticle Size and Protein Charge Affect Gold Nanoparticle-Protein Interactions?

When exposed to a solution containing gold nanoparticles (AuNPs), proteins spontaneously bind to the nanoparticle surface, leading to the formation of a stable surface coating, or biocorona. The composition of this biocorona in biological fluids depends on various factors, and it is currently impossible to predict whether an adsorbed protein will retain its function on the AuNP surface. AuNPs are potentially useful in a variety of diagnostic and therapeutic applications, but it is necessary to understand the physical interaction with host proteins before any of these applications can be realized. Using biophysical NMR spectroscopy, we are investigating the structural consequences and thermodynamic determinants of protein-nanoparticle interactions. Using a dataset of six globular proteins, we have found that all of them appear to remain globular upon binding, forming a single layer on the nanoparticle surface. Protein hydrogen-deuterium exchange rates are not perturbed upon addition of AuNPs, suggesting that at least some native structure is retained on the surface. Our observations hold for a broad range of nanoparticle sizes, suggesting that surface curvature may only play a minor role in protein binding. Most recently, we have investigated protein binding as a function of pH, and, assuming moderate shifts in protein pKa values, we have derived a thermodynamic model for the electrostatic contribution to binding. This model can be used to interpret competition experiments where two proteins are exposed to the same nanoparticle. From our results, we conclude that binding is a complex, electrostatically-driven process with multiple discrete steps. Future investigations will focus on whether the principles derived here can be used to design functional protein-based nanoconjugates.

Dynamic expression of miRNAs across immature and adult stages of the malaria mosquito Anopheles stephensi

BackgroundMicroRNAs are small non-coding RNAs that are involved in various biological processes including insect development. Anopheles stephensi serves as primary vector of malaria parasite in Asia and exhibits holometabolous life cycle that involves four different stages of development. Regulation and role of mosquito miRNAs during various stages of mosquito development remain largely unknown.MethodsHigh throughput small RNA sequencing was employed for identification and profiling of miRNAs across immature and adult stages of malaria vector, which were further validated using Northern hybridization and real time PCR. Target prediction and pathway analysis was carried out to understand the role of regulated miRNAs in insect development. Degradome sequencing was employed to identify cleaved targets of some regulated miRNAs. Loss of function strategy was employed for miR-989 to understand its probable role in female reproductive process.ResultsSmall RNA sequencing and data analysis revealed 111 and 14 known and novel miRNAs respectively across all stages of Anopheles stephensi. Nine miRNAs showed gender specific regulation across different stages of mosquito development. Analysis of miRNAs revealed regulation of 24 and 26 miRNAs across different stages of male and female mosquito development respectively. mRNA targets and significant pathways targeted by regulated miRNAs were identified for each stage of mosquito development. Degradome sequencing revealed twenty nine cleaved targets of insect miRNAs. MicroRNA-989 showed significant up-regulation in the adult female as compared to adult male mosquito. Knockdown of miR-989 expression in adult female using miRNA specific antagomir affected targets playing roles in protein binding, proteolysis and nucleic acid binding in ovary tissue of female mosquito post blood feeding.ConclusionsThis is the first comprehensive effort to understand regulation of Anopheles stephensi miRNAs across developmental stages of male and female mosquito. Preliminary role of regulated miRNAs in mosquito development was revealed by target prediction and pathway analysis. MicroRNA-989 emerged to have important roles in adult female mosquitoes showing significant up-regulation which was further studied using miR-989 specific antagomir. This study provides insights into mosquito development and reproductive process and has implications for effective control of mosquito population required for reducing spread of mosquito-borne infectious diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-015-0772-y) contains supplementary material, which is available to authorized users.

Binding of a chromen-4-one Schiff’s base with bovine serum albumin: capping with β-cyclodextrin influences the binding

This work deals with the synthesis of 6-methyl-3-[(4′-methylphenyl)imino]methyl-4H-chromen-4-one (MMPIMC), its binding to β-cyclodextrin, and the influence of the cyclodextrin complexation on the compound’s binding to bovine serum albumin (BSA). The 1:2 stoichiometry for the complexation of MMPIMC with β-cyclodextrin is determined with the binding constant of 1.90 × 104 M−2. The structure of host–guest complex plays a role in protein binding of MMPIMC. One- and two-dimensional NMR spectra are used to determine the mode of binding of the guest to β-cyclodextrin cavity and the structure of the inclusion complex is proposed. The binding of MMPIMC with BSA in the absence and the presence of β-cyclodextrin is studied. The binding strengths of MMPIMC–BSA (1.73 × 105 M−1) and β-cyclodextrin-complexed MMPIMC–BSA (9.0 × 104 M−1) show difference in magnitude. The Förster Resonance Energy Transfer efficiency and the proximity of the donor and acceptor molecules, are modulated by β-cyclodextrin. Molecular modeling is used to optimize the sites and mode of binding of MMPIMC with bovine serum albumin.

The effect of Pot1 binding on the repair of thymine analogs in a telomeric DNA sequence.

Telomeric DNA can form duplex regions or single-stranded loops that bind multiple proteins, preventing it from being processed as a DNA repair intermediate. The bases within these regions are susceptible to damage; however, mechanisms for the repair of telomere damage are as yet poorly understood. We have examined the effect of three thymine (T) analogs including uracil (U), 5-fluorouracil (5FU) and 5-hydroxymethyluracil (5hmU) on DNA–protein interactions and DNA repair within the GGTTAC telomeric sequence. The replacement of T with U or 5FU interferes with Pot1 (Pot1pN protein of Schizosaccharomyces pombe) binding. Surprisingly, 5hmU substitution only modestly diminishes Pot1 binding suggesting that hydrophobicity of the T-methyl group likely plays a minor role in protein binding. In the GGTTAC sequence, all three analogs can be cleaved by DNA glycosylases; however, glycosylase activity is blocked if Pot1 binds. An abasic site at the G or T positions is cleaved by the endonuclease APE1 when in a duplex but not when single-stranded. Abasic site formation thermally destabilizes the duplex that could push a damaged DNA segment into a single-stranded loop. The inability to enzymatically cleave abasic sites in single-stranded telomere regions would block completion of the base excision repair cycle potentially causing telomere attrition.

Prediction of hot spots residues in protein–protein interface using network feature and microenvironment feature

Hot spots residues in protein–protein interface play crucial roles in protein binding. In the present study, complex network method was applied to uncover influence of neighboring residues on hot spots and then several network and microenvironment features were designed to describe the diversity of environment of hot spots. After feature analysis by permutation importance in Random Forest (RF), an optimal 58-dimensional feature set including ten network and microenvironment features was selected and then applied to construct a Support Vector Machine (SVM) prediction model for hot spots. A satisfactory accuracy (ACC) value of 79.0% and a Mathew's correlation coefficient (MCC) value of 0.470 were obtained for independent test set. The novel network features and microenvironment features were proved to be promising in discovering hot spots in interfaces. A further microenvironment analysis was also performed. Amino acid residues directly contacting with hot spots in residue–residue interaction network exhibit significant importance for the microenvironment of hot spots. Amino acid alanine (A), aspartic acid (D), glycine (G), histidine (H), isoleucine (I), asparagine (N), serine (S) and tyrosine (Y) are more likely to occur in the vicinity of hot spots than in the vicinity of non-hot spots. These amino acid residues probably cluster together to construct a proper microenvironment for hot spots.

Structural and Functional Characterization of Mature Forms of Metalloprotease E495 from Arctic Sea-Ice Bacterium Pseudoalteromonas sp. SM495

E495 is the most abundant protease secreted by the Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. As a thermolysin family metalloprotease, E495 was found to have multiple active forms in the culture of strain SM495. E495-M (containing only the catalytic domain) and E495-M-C1 (containing the catalytic domain and one PPC domain) were two stable mature forms, and E495-M-C1-C2 (containing the catalytic domain and two PPC domains) might be an intermediate. Compared to E495-M, E495-M-C1 had similar affinity and catalytic efficiency to oligopeptides, but higher affinity and catalytic efficiency to proteins. The PPC domains from E495 were expressed as GST-fused proteins. Both of the recombinant PPC domains were shown to have binding ability to proteins C-phycocyanin and casein, and domain PPC1 had higher affinity to C-phycocyanin than domain PPC2. These results indicated that the domain PPC1 in E495-M-C1 could be helpful in binding protein substrate, and therefore, improving the catalytic efficiency. Site-directed mutagenesis on the PPC domains showed that the conserved polar and aromatic residues, D26, D28, Y30, Y/W65, in the PPC domains played key roles in protein binding. Our study may shed light on the mechanism of organic nitrogen degradation in the Arctic sea ice.

Adsorption induced enzyme denaturation: The role of protein surface in adsorption induced protein denaturation on allyl glycidyl ether (AGE)–ethylene glycol dimethacrylate (EGDM) copolymers

The effects of protein size on adsorption and adsorption-induced denaturation of proteins on copolymers of allyl glycidyl ether (AGE)–ethylene glycol dimethacrylate (EGDM) have been studied. Different responses were observed for the amount of protein adsorbed and denatured on the polymer surface for different proteins (trypsin, alchol dehydrogenase from baker's yeast (YADH), glucose dehydrogenase (GDH) from Gluconobacter cerinus, and alkaline phosphates from calf intestinal mucosa (CIAP). Protein adsorption on the copolymer with 25% crosslink density (AGE-25) was dependent not only on the size of the protein but also on the presence of glycoside residues on the protein surface. Adsorption and denaturation of proteins follows the order YADH > trypsin > GDH ≫ CIAP although the molecular weights of the proteins follow the order YADH > CIAP > GDH > trypsin. The lack of correlation between amount of adsorbed protein and its molecular weight was due to the presence of glycoside residues on CIAP and GDH which protect the enzyme surface from denaturation. Enzyme stabilities in aqueous solutions of 1-cyclohexyl-2-pyrrolidinone (CHP) correlate well with the trend in denaturation by the copolymer, strongly suggesting that hydrophobic interactions play a major role in protein binding and the mechanism of protein denaturation is similar to that for water–miscible organic solvents.

Specific Basic and Aromatic Residues Optimize the Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein

As an efficient nucleic acid chaperone protein, the human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein facilitates the rearrangement of nucleic acid secondary structure during reverse transcription and recombination. The biophysical basis for NC's chaperone activity includes the ability to strongly aggregate nucleic acids, destabilize nucleic acid secondary structure, and facilitate rapid protein-nucleic acid interaction kinetics. HIV-1 NC contains only 55 amino acids, with 11 basic residues throughout its structure as well as two zinc fingers, each having a single aromatic residue (F16 and W37), which is highly conserved among retroviral NC proteins. Despite its simple structure, HIV-1 NC facilitates nucleic acid rearrangement efficiently. To determine the mechanism behind this high efficiency, we performed single-molecule DNA stretching experiments in the presence of wild-type and mutant HIV-NC. We measured the ability of the proteins to aggregate and destabilize dsDNA and determined their ability to facilitate nucleic acid annealing. We show that mutant F16W and F16W-W37F exhibit similar properties as wild-type NC. In contrast, the single aromatic substitutions W37A and F16A significantly reduce NC's rapid DNA interaction kinetics, while retaining a portion of its dsDNA destabilization capability. Furthermore, removing both aromatics leads to a complete loss of chaperone activity. Thus, we can conclude that both aromatic residues significantly contribute to HIV-1 NC's optimal chaperone activity. Moreover, experiments on basic residue mutants show that positively charged residues play a very important role in protein binding. While mutating basic residues in any region of the protein significantly reduces reannealing kinetics, residues in the zinc fingers and in the N-terminus are particularly important for rapid protein-nucleic acid interaction kinetics. This work was funded in part by Federal Funds from NCI, NIH under contract N01-CO-12400 (RJG).