Pro Residues Research Articles

Construction and Characterization of Novel Hirulog Variants with Antithrombin and Antiplatelet Activities

The RGD sequence was used to design potent hirudin isoform 3 mimetic peptides with both antithrombin activity and antiplatelet aggregation activity. The RGD and proline were inserted between the catalytic active binding domain (D-Phe-Pro-Arg-Pro) on the N-terminus and the anion-binding exosite binding domain (QGDFEPIPEDAYDE) on the Cterminus. Thrombin titration assay and ATP-induced platelet aggregation test revealed that the peptide with the linker RGDWP or RGDGP possessed potent antithrombin and antiplatelet activities, while other peptides without the Pro residue in the linker only showed antithrombin activity. Similar results were obtained in the RGD-containing hirulog-1 variants. Our study indicates that the inserted Pro residue facilitates the exposure of RGD and the binding of the peptide to glycoprotein IIb/IIIa (GPIIb/IIIa). The strategy of combining the RGD sequence and the Pro residue may be used for future designs of bifunctional antithrombotic agents.

P-I class metalloproteinase from Bothrops moojeni venom is a post-proline cleaving peptidase with kininogenase activity: Insights into substrate selectivity and kinetic behavior

Snake venom metalloproteinases (SVMPs) belonging to P-I class are able to hydrolyze extracellular matrix proteins and coagulation factors triggering local and systemic reactions by multiple molecular mechanisms that are not fully understood. BmooMPα-I, a P-I class SMVP from Bothrops moojeni venom, was active upon neuro- and vaso-active peptides including angiotensin I, bradykinin, neurotensin, oxytocin and substance P. Interestingly, BmooMPα-I showed a strong bias towards hydrolysis after proline residues, which is unusual for most of characterized peptidases. Moreover, the enzyme showed kininogenase activity similar to that observed in plasma and cells by kallikrein. FRET peptide assays indicated a relative promiscuity at its S2–S′2 subsites, with proline determining the scissile bond. This unusual post-proline cleaving activity was confirmed by the efficient hydrolysis of the synthetic combinatorial library MCA-GXXPXXQ-EDDnp, described as resistant for canonical peptidases, only after Pro residues. Structural analysis of the tripeptide LPL complexed with BmooMPα-I, generated by molecular dynamics simulations, assisted in defining the subsites and provided the structural basis for subsite preferences such as the restriction of basic residues at the S2 subsite due to repulsive electrostatic effects and the steric impediment for large aliphatic or aromatic side chains at the S1 subsite. These new functional and structural findings provided a further understanding of the molecular mechanisms governing the physiological effects of this important class of enzymes in envenomation process.

Insights into cardiovascular effects of proline-rich oligopeptide (Bj-PRO-10c) revealed by structure–activity analyses: dissociation of antihypertensive and bradycardic effects

We have previously reported that the proline-rich decapeptide from Bothrops jararaca (Bj-PRO-10c) causes potent and sustained antihypertensive and bradycardic effects in SHR. These activities are independent of ACE inhibition. In the present study, we used the Ala-scan approach to evaluate the importance of each amino acid within the sequence of Bj-PRO-10c (Pyr(1)-Asn(2)-Trp(3)-Pro(4)-His(5)-Pro(6)-Gln(7)-Ile(8)-Pro(9)-Pro(10)). The antihypertensive and bradycardic effects of the analogues Bj-PRO-10c Ala(3), Bj-PRO-10c Ala(7), Bj-PRO-10c Ala(8) were similar to those of Bj-PRO-10c, whereas the analogues Bj-PRO-10c Ala(2), Bj-PRO-10c Ala(4), Bj-PRO-10c Ala(5), Bj-PRO-10c Ala(9), and Bj-PRO-10c Ala(10) kept the antihypertensive activity and lost bradycardic activity considerably. In contrast, Bj-PRO-10c Ala(1) and Bj-PRO-10c Ala(6) were unable to provoke any cardiovascular activity. In summary, we demonstrated that (1) the Pyr(1) and Pro(6) residues are essential for both, the antihypertensive and bradycardic effects of Bj-PRO-10c; (2) Ala-scan approach allowed dissociating blood pressure reduction and bradycardic effects.Conformational properties of the peptides were examined by means of circular dichroism (CD) spectroscopy. The different Ala-scan analogues caused either an increase or decrease in the type II polyproline helix content compared to Bj-PRO-10c. The complete loss of activity of the Pro(6)→Ala(6) mutant is probably due to the fact that in the parent peptide the His(5)-Pro(6) bond can exist in the cis configuration, which could correspond to the conformation of this bond in the bound state. Current data support the Bj-PRO-10c as a promising leader prototype to develop new agents to treat cardiovascular diseases and its co-morbidities.

Rescuing Biological Activity from Synthetic Phakellistatin 19

Phakellistatins is one of the families of Pro-rich cyclic peptides whose synthetic counterparts have revealed cytotoxicities that differ greatly from those displayed by their corresponding natural ones. This is also the case of the last member isolated from this family, phakellistatin19, an octacyclopeptide containing three Pro moieties and a high percentage of apolar residues. Exhaustive NMR studies on the synthetic and natural phakellistatin 19 have been performed in order to find a plausible explanation for this intriguing behavior. Moreover, taking advantage of phakellistatin's framework, analogues with different cis/trans geometry at the key prolyl peptide bonds were designed, covering a promising conformational space that could not be reached by the natural peptide. By introduction of proline surrogates (Ψ(Me,Me)pro residues) in phakellistatin 19, which effectively increases the percentage of cis conformation in the final peptides, this translates into enhanced biological activity, therefore "rescuing" an otherwise inactive cyclopeptide.

Site‐Directed Spin Labeling of a Collagen Mimetic Peptide

Collagen as the most abundant protein in mammals consists of three chains that are built up of repeating Xaa-YaaGly units with all peptide bonds in trans conformation and most often with proline in Xaa and (4R)-hydroxyproline in the Yaa position. This type of sequence favors a lefthanded poly-Pro-II helix conformation and the intertwining of the three chains into the unique right-handed triple helix. The X-ray structure analysis of collagen mimetic peptides (CMPs) of repeating Xaa-Yaa-Gly triplets show Cendo puckers of the Pro residues in Xaa and C-exo puckers of the Hyp residues in Yaa position. Studies on structural factors that stabilize the triple helical fold with proline derivatives led to the conclusion that besides the interchain hydrogen bond between the NH group of Gly of one strand and the CO group of Pro of the adjacent strand, stereoelectronic effects that favor the all trans-peptide bond conformation and the correct puckering are decisively affecting the structural stability. Recent studies by Erdman and Wennemers with proline derivatives in the Yaa position that exhibit preferences for the C-endo puckering, but a trans amide conformer, contradict this conclusion showing that the ring puckering is less important for the stability of collagen if the trans/cis amide conformer ratio favors formation of the triple helix. The aim of the present study was to investigate whether electron spin resonance spectroscopy (ESR) could yield new information on the dynamics of triple helix folding/unfolding as a useful alternative to the other spectroscopic techniques applied so far. Indeed this type of spectroscopy has become popular for studying conformational changes and unfolding processes of proteins as many ESR spectral parameters, such as peak-to-peak height, peak-to-peak width and rotational correlation time can accurately reflect relative mobility and environmental changes of spin labels (Figure 1). For the design and synthesis of a suitable spin-labeled CMP, the results of a recent detailed study on the equilibrium constants of acetyl-(4R)-Pro(X)-OMe (X=ammonium or acetylamide) by NMR spectroscopy were taken into account. Although for the ammonium derivative a significantly reduced preference for the trans conformation was observed, a trans conformer preference similar to that of (4R)hydroxyproline was recovered upon acetylation of the gamino group. Correspondingly, Ac-(Gly-Pro-Hyp)7-Gly-GlyNH2 [7] was selected as the CMP in which the Hyp residue of the central triplet was replaced by (2S,4R)-aminoproline [a] J. Jiang, Q. Jin, W. Ma, Prof. Dr. S. Dong School of Life Sciences, Lanzhou University 222 Tianshui South Road, Lanzhou 730000 (China) E-mail : dongsl@lzu.edu.cn [b] L. Yang Department of Medical Laboratory and Research Center Tangdu Hospital, Fourth Military Medical University Xi’an 710038 (China) [c] Prof. Dr. L. Moroder Bioorganic Chemistry, Max Planck Institute of Biochemistry Am Klopferspitz 18, 82152 Martinsried (Germany) [d] Prof. Dr. S. Dong Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, 222 Tianshui South Road Lanzhou 730000 (China) [] These authors contributed equally to this work. Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.201303290. Figure 1. The relative mobility and environmental changes of spin labels with collagen folded/unfolded states.

Cloning and expression profiling of odorant‐binding proteins in the tarnished plant bug, Lygus lineolaris

In insects, the perception and discrimination of odorants requires the involvement of odorant-binding proteins (OBPs). To gain a better molecular understanding of olfaction in the agronomic pest Lygus lineolaris (the tarnished plant bug), we used a transcriptomics-based approach to identify potential OBPs. In total, 33 putative OBP transcripts, including the previously reported Lygus antennal protein (LAP), were identified based on the characteristic OBP Cys signature and/or sequence similarity with annotated orthologous sequences. The L. lineolaris OBP (LylinOBP) repertoire consists of 20 'classic' OBPs, defined by the spacing of six conserved Cys residues, and 12 'Plus-C' OBPs, defined by the spacing of eight conserved Cys and one conserved Pro residue. Alternative splicing of OBP genes appears to contribute significantly to the multiplicity of LylinOBP sequences. Microarray-based analysis of chemosensory tissues (antennae, legs and proboscis) revealed enrichment of 21 LylinOBP transcripts in antennae, 12 in legs, and 15 in proboscis, suggesting potential roles in olfaction and gustation respectively. PCR-based determination of transcript abundance for a subset of the LylinOBP genes across multiple adult tissues yielded results consistent with the hybridization data.

Enhancement in the rate of conversion of peptide Cys-Pro esters to peptide thioesters by structural modification

We previously reported that the peptide containing a Cys-Pro ester (CPE) moiety is spontaneously transformed into a peptide thioester via an N to S acyl shift followed by diketopiperazine formation. In an attempt to identify more reactive structures for the formation of a peptide thioester, we modified the CPE structure, in which the Pro residue in the CPE moiety was replaced with N-substituted glycine derivatives. These peptides were transformed into a peptide thioester more rapidly. Alternatively, the addition of an amino acid residue at the C-terminus of the CPE moiety also accelerated thioester formation.

The importance of being kinked: role of Pro residues in the selectivity of the helical antimicrobial peptide P5

Antimicrobial peptides (AMPs) are promising compounds for developing new antibiotic drugs against drug-resistant bacteria. Many of them kill bacteria by perturbing their membranes but exhibit no significant toxicity towards eukaryotic cells. The identification of the features responsible for this selectivity is essential for their pharmacological development. AMPs exhibit few conserved features, but a statistical analysis of an AMP sequence database indicated that many α-helical AMPs surprisingly have a helix-breaking Pro residue in the middle of their sequence. To discriminate among the different possible hypotheses for the functional role of this feature, we designed an analogue of the antimicrobial peptide P5, in which the central Pro was deleted (analogue P5Del). Pro removal resulted in a dramatic increase of toxicity. This was explained by the observation that P5Del binds both charged and neutral membranes, whereas P5 has no appreciable affinity towards neutral bilayers. CD and simulative data provided a rationalization of this behavior. In solution P5, due to the presence of Pro, attains compact conformations, in which its apolar residues are partially shielded from the solvent, whereas P5Del is more helical. These structural differences reduce the hydrophobic driving force for association of P5 to neutral membranes, whereas its binding to anionic bilayers can still take place because of electrostatic attraction. After membrane binding, the Pro residue does not preclude the attainment of a membrane-active amphiphilic helical conformation. These findings shed light on the role of Pro residues in the selectivity of AMPs and provide hints for the design of new, highly selective compounds.

Structural and mechanistic insights into collagen degradation by a bacterial collagenolytic serine protease in the subtilisin family

A number of proteases in the subtilisin family derived from environmental or pathogenic microorganisms have been reported to be collagenolytic serine proteases. However, their collagen degradation mechanisms remain unclear. Here, the degradation mechanism of type I collagen fibres by the S8 collagenolytic protease MCP-01, from Pseudoalteromonas sp. SM9913, was studied. Atomic force microscopy observation and biochemical analysis confirmed that MCP-01 progressively released single fibrils from collagen fibres and released collagen monomers from fibrils mainly by hydrolysing proteoglycans and telopeptides in the collagen fibres. Structural and mutational analyses indicated that an enlarged substrate-binding pocket, mainly composed of loops 7, 9 and 11, is necessary for collagen recognition and that the acidic and aromatic residues on these loops form a negatively charged, hydrophobic environment for collagen binding. MCP-01 displayed a non-strict preference for peptide bonds with Pro or basic residues at the P1 site and/or Gly at the P1' site in collagen. His211 is a key residue for the P1-basic-residue preference of MCP-01. Our study gives structural and mechanistic insights into collagen degradation of the S8 collagenolytic protease, which is helpful in developing therapeutics for diseases with S8 collagenolytic proteases as pathogenic factors and in studying environmental organic nitrogen degradation mechanisms.

FK506-Binding Protein 12 Modulatesμ-Opioid Receptor Phosphorylation and Protein Kinase Cε–Dependent Signaling by Its Direct Interaction with the Receptor

Protein kinase C (PKC) activation plays an important role in morphine-induced μ-opioid receptor (OPRM1) desensitization and tolerance development. It was recently shown that receptor phosphorylation by G protein-coupled receptor kinase regulates agonist-dependent selective signaling and that inefficient phosphorylation of OPRM1 leads to PKCε activation and subsequent responses. Here, we demonstrate that such receptor phosphorylation and PKCε activation can be modulated by FK506-binding protein 12 (FKBP12). Using a yeast two-hybrid screen, FKBP12 was identified as specifically interacting with OPRM1 at the Pro(353) residue. In human embryonic kidney 293 cells expressing OPRM1, the association of FKBP12 with OPRM1 decreased the agonist-induced receptor phosphorylation at Ser(375). The morphine-induced PKCε activation and the recruitment of PKCε to the OPRM1 signaling complex were attenuated both by FKBP12 short interfering RNA (siRNA) treatment and in cells expressing OPRM1 with a P353A mutation (OPRM1P353A), which leads to diminished activation of PKC-dependent extracellular signal-regulated kinases. Meanwhile, the overexpression of FKBP12 enabled etorphine to activate PKCε. Further analysis of the receptor complex demonstrated that morphine treatment enhanced the association of FKBP12 and calcineurin with the receptor. The blockade of the FKBP12 association with the receptor by the siRNA-mediated knockdown of endogenous FKBP12 or the mutation of Pro(353) to Ala resulted in a reduction in PKCε and calcineurin recruitment to the receptor signaling complex. The receptor-associated calcineurin modulates OPRM1 phosphorylation, as demonstrated by the ability of the calcineurin autoinhibitory peptide to increase the receptor phosphorylation. Thus, the association of FKBP12 with OPRM1 attenuates the phosphorylation of the receptor and triggers the recruitment and activation of PKCε.

N-Terminal methylation of proteasome subunit Rpt1 in yeast

The 26S proteasome is a multicatalytic protease complex that degrades ubiquitinated proteins in eukaryotic cells. It consists of a proteolytic core (the 20S proteasome) as well as regulatory particles, which contain six ATPase (Rpt) subunits involved in unfolding and translocation of substrates to the catalytic chamber of the 20S proteasome. In this study, we used MS to analyze the N-terminal modifications of the yeast Rpt1 subunit, which contains the N-terminal recognition sequence for N-methyltransferase. Our results revealed that following the removal of the initiation Met residue of yeast Rpt1, the N-terminal Pro residue is either unmodified, mono-methylated, or di-methylated, and that this N-methylation has not been conserved throughout evolution. In order to gain a better understanding of the possible function(s) of the Pro-Lys (PK) sequence at positions 3 and 4 of yeast Rpt1, we generated mutant strains expressing an Rpt1 allele that lacks this sequence. The absence of the PK sequence abolished N-methylation, decreased cell growth, and increased sensitivity to stress. Our data suggest that N-methylation of Rpt1 and/or its PK sequence might be important in cell growth or stress tolerance in yeast.

Susceptibility of milk protein-derived peptides to dipeptidyl peptidase IV (DPP-IV) hydrolysis

In silico digestion of milk protein-derived peptides with gastrointestinal enzyme activities was used to predict the release of peptides with a Pro residue at position 2 from the N terminus. These peptides are known to act as preferred dipeptidyl peptidase IV (DPP-IV) substrates. Five casein-derived synthetic peptides (Ile-Pro-Ile-Gln-Tyr, Leu-Pro-Leu-Pro-Leu, Tyr-Pro-Tyr-Tyr, Leu-Pro-Tyr-Pro-Tyr and Ile-Pro-Ile) and a casein (CasH), whey (WPH) and lactoferrin hydrolysate (LFH) generated with gastrointestinal enzymes were incubated with DPP-IV at 37°C for 18 or 24h. Peptide breakdown was evident following incubation with DPP-IV. Different modes of DPP-IV inhibition were observed depending on the test compound. Ile-Pro-Ile-Gln-Tyr, Tyr-Pro-Tyr-Tyr and Leu-Pro-Tyr-Pro-Tyr were substrate-, Leu-Pro-Leu-Pro-Leu and CasH were prodrug- while WPH and LFH were true DPP-IV inhibitors. These results are relevant for the bioactivity and bioavailability of functional foods targeting DPP-IV inhibition with potential blood glucose regulatory properties in humans.

Elongation factor P: Function and effects on bacterial fitness

The elongation phase of translation is promoted by three universal elongation factors, EF-Tu, EF-Ts, and EF-G in bacteria and their homologs in archaea and eukaryotes. Recent findings demonstrate that the translation of a subset of mRNAs requires a fourth elongation factor, EF-P in bacteria or the homologs factors a/eIF5A in other kingdoms of life. EF-P prevents the ribosome from stalling during the synthesis of proteins containing consecutive Pro residues, such as PPG, PPP, or longer Pro clusters. The efficient and coordinated synthesis of such proteins is required for bacterial growth, motility, virulence, and stress response. EF-P carries a unique post-translational modification, which contributes to its catalytic proficiency. The modification enzymes, which are lacking in higher eukaryotes, provide attractive new targets for the development of new, highly specific antimicrobials.

Prokaryotic Selectivity, Bactericidal Mechanism and LPS-neutralizing Activity of Lys-linked Dimeric Peptide of Indolicidin C-terminal Hexapeptide

Indolicidin (Ind) is a cationic antimicrobial peptide (AMP) derived from the granules of bovine neutrophils. It is a short, 13 amino acid peptide (ILPWKWPWWPWRR-NH2) that is amidated at the C-terminus and contains the highest proportion of Trp and Pro residues. Like many other AMPs, it exhibits a broad spectrum of antimicrobial activity against bacteria, fungi and protozoa. It has been shown that Ind adopts a disordered conformation in solution and a membrane-interacting structure containing coils and turns. However, Ind exhibits some toxicity to human erythrocytes and mouse T lymphocytes. In the present study, to investigate the effect of Lys-linked dimerization of Ind C-terminal hexapeptide (WWPWRRNH2) on prokaryotic selectivity, bactericidal mechanism and LPS-neutralizing activity and to develop a novel short AMP having prokaryotic selectivity and LPS-neutralizing activity, we synthesized a Lys-linked dimeric peptide (di-Ind-6) of Ind C-terminal hexapeptide (Ind-6) (Table 1). We examined the antimicrobial activity of the peptides against a representative set of bacterial strains, including three Gram-negative bacteria (Escherichia coli [KCTC 1682], Pseudomonas aeruginosa [KCTC 1637] and Salmonella typhimurium [KCTC 1926]) and three Gram-positive bacteria (Bacillus subtilis [KCTC 3068], Staphylococcus epidermidis [KCTC 1917] and Staphylococcus aureus [KCTC 1621]). The MIC values of the peptides are shown in Table 2. A Lys-linked dimeric peptide (di-Ind-6) displayed 2to 4-fold increased antimicrobial activity compared to monomeric peptide (Ind6). Furthermore, Di-Ind-6 displayed a 2-fold enhanced antimicrobial activity against Gram-negative bacteria as compare to Ind. Next, the cytotoxicity of the peptides to mammalian cells was determined by measuring their hemolytic activity toward human red blood cells (h-RBCs) Concentrationresponse curves for the hemolytic activity of the peptides are shown in Figure 1. For a quantitative measure of the hemolytic activity of the peptides, we introduced the hemolytic concentration (HC50) defined as the lowest peptide concentration that produces 50% hemolysis (Table 3). The HC50 value for Ind and di-Ind-6 was 160 μg/mL and 192 μg/mL, respectively. Di-Ind-6 was somewhat less hemolytic than Ind. In contrast, Ind-6 did not induce hemolysis even at the highest peptide concentration tested (200 μg/mL). The therapeutic potential of peptide antimicrobial drugs lies in their prokaryotic selectivity to effectively kill bacterial cells without exhibiting significant cytotoxicity toward mammalian cells such as human red blood cells. To determine prokaryotic selectivity of the peptides, we calculated their therapeutic index (TI) (Table 3). The TI is a widely employed parameter to represent the specificity of antimicrobial agents. The TI of the peptides is calculated as the ratio of the HC50 to GM (geometric mean of MICs against six selected Table 1. Amino acid sequences and calculated and observed molecular masses of the peptides

Structure-Activity Relationship of Synthetic Variants of the Milk-Derived Antimicrobial Peptide α s2 -Casein f(183–207)

Template-based studies on antimicrobial peptide (AMP) derivatives obtained through manipulation of the amino acid sequence are helpful to identify properties or residues that are important for biological activity. The present study sheds light on the importance of specific amino acids of the milk-derived αs2-casein f(183-207) peptide to its antibacterial activity against the food-borne pathogens Listeria monocytogenes and Cronobacter sakazakii. Trimming of the peptide revealed that residues at the C-terminal end of the peptide are important for activity. Removal of the last 5 amino acids at the C-terminal end and replacement of the Arg at position 23 of the peptide sequence by an Ala residue significantly decreased activity. These findings suggest that Arg23 is very important for optimal activity of the peptide. Substitution of the also positively charged Lys residues at positions 15 and 17 of the αs2-casein f(183-207) peptide also caused a significant reduction of the effectiveness against C. sakazakii, which points toward the importance of the positive charge of the peptide for its biological activity. Indeed, simultaneous replacement of various positively charged amino acids was linked to a loss of bactericidal activity. On the other hand, replacement of Pro residues at positions 14 and 20 resulted in a significantly increased antibacterial potency, and hydrophobic end tagging of αs2-casein f(193-203) and αs2-casein f(197-207) peptides with multiple Trp or Phe residues significantly increased their potency against L. monocytogenes. Finally, the effect of pH (4.5 to 7.4), temperature (4°C to 37°C), and addition of sodium and calcium salts (1% to 3%) on the activity of the 15-amino-acid αs2-casein f(193-207) peptide was also determined, and its biological activity was shown to be completely abolished in high-saline environments.

PASylation: a biological alternative to PEGylation for extending the plasma half-life of pharmaceutically active proteins

A major limitation of biopharmaceutical proteins is their fast clearance from circulation via kidney filtration, which strongly hampers efficacy both in animal studies and in human therapy. We have developed conformationally disordered polypeptide chains with expanded hydrodynamic volume comprising the small residues Pro, Ala and Ser (PAS). PAS sequences are hydrophilic, uncharged biological polymers with biophysical properties very similar to poly-ethylene glycol (PEG), whose chemical conjugation to drugs is an established method for plasma half-life extension. In contrast, PAS polypeptides offer fusion to a therapeutic protein on the genetic level, permitting Escherichia coli production of fully active proteins and obviating in vitro coupling or modification steps. Furthermore, they are biodegradable, thus avoiding organ accumulation, while showing stability in serum and lacking toxicity or immunogenicity in mice. We demonstrate that PASylation bestows typical biologics, such as interferon, growth hormone or Fab fragments, with considerably prolonged circulation and boosts bioactivity in vivo.

EIF5A Promotes Translation of Polyproline Motifs

Translation factor eIF5A, containing the unique amino acid hypusine, was originally shown to stimulate Met-puromycin synthesis, a model assay for peptide bond formation. More recently, eIF5A was shown to promote translation elongation; however, its precise requirement in protein synthesis remains elusive. We use in vivo assays in yeast and in vitro reconstituted translation assays to reveal a specific requirement for eIF5A to promote peptide bond formation between consecutive Pro residues. Addition of eIF5A relieves ribosomal stalling during translation of three consecutive Pro residues in vitro, and loss of eIF5A function impairs translation of polyproline-containing proteins in vivo. Hydroxyl radical probing experiments localized eIF5A near the E site of the ribosome with its hypusine residue adjacent to the acceptor stem of the P site tRNA. Thus, eIF5A, like its bacterial ortholog EFP, is proposed to stimulate the peptidyl transferase activity of the ribosome and facilitate the reactivity of poor substrates like Pro.

Solution Structure and In Silico Binding of a Cyclic Peptide with Hepatitis B Surface Antigen

A specific ligand targeting the immunodominant region of hepatitis B virus is desired in neutralizing the infectivity of the virus. In a previous study, a disulfide constrained cyclic peptide cyclo S(1) ,S(9) Cys-Glu-Thr-Gly-Ala-Lys-Pro-His-Cys (S(1) , S(9) -cyclo-CETGAKPHC) was isolated from a phage displayed cyclic peptide library using an affinity selection method against hepatitis B surface antigen. The cyclic peptide binds tightly to hepatitis B surface antigen with a relative dissociation constant (KD (rel) ) of 2.9nm. The binding site of the peptide was located at the immunodominant region on hepatitis B surface antigen. Consequently, this study was aimed to elucidate the structure of the cyclic peptide and its interaction with hepatitis B surface antigen in silico. The solution structure of this cyclic peptide was solved using (1) H, (13) C, and (15) N NMR spectroscopy and molecular dynamics simulations with NMR-derived distance and torsion angle restraints. The cyclic peptide adopted two distinct conformations due to the isomerization of the Pro residue with one structured region in the ETGA sequence. Docking studies of the peptide ensemble with a model structure of hepatitis B surface antigen revealed that the cyclic peptide can potentially be developed as a therapeutic drug that inhibits the virus-host interactions.

Probing insect odorant receptors with their cognate ligands: Insights into structural features

Odorant receptors (ORs) are essential for insect survival in the environment and thus are ideal molecular targets for the design of insect-inspired modern green chemicals to control populations of agricultural pests and insects of medical importance. Although insect ORs are known for more than a decade, their structural biology is still in its infancy. Here, we unravel the first structural features of ORs from the malaria mosquito, the Southern house mosquito and the silkworm moth. The second extracellular loops (ECL-2s) of their predicted structures are much longer than ECL-1s and ECL-3s. The 27 amino-acid-residue-long of the ECL-2s in mosquito and the 43 amino-acid-residue-long ECL2s in moth ORs are well-conserved. About one-third of the residues are identical, including 3–4 Pro residues. Thorough examination of well-conserved residues in these structures, by point mutation and functional assay with the Xenopus oocyte recording system, strongly suggest that these “loops” include three β-turns and some degree of folding. In the Southern house mosquito three Pro residues in ECL-2 are essential for full activation of the receptor, which is finely tuned to the oviposition attractant 3-methylindole. Additionally, the “corner residues” of prolines, including Gly, Tyr, and Leu are functionally important thus suggesting that turns are stabilized not only by backbone hydrogen bonds, but also by side–chain interactions. Examination of ECL-2s from a distant taxonomical group suggests these ECL-2 loops might be functionally important in all insect ORs. Two of the four Pro residues in the predicted ECL-2 of the bombykol receptor in the silkworm moth, BmorOR1, are essential for function. Experimental evidence indicates that these loops may not be specificity determinants, but they may form a cover to the yet-to-be-identified membrane embedded binding cavities of insect ORs.

Dissecting the Metal Selectivity of MerR Monovalent Metal Ion Sensors in Salmonella

Two homologous transcription factors, CueR and GolS, that belong to the MerR metalloregulatory family are responsible for Salmonella Cu and Au sensing and resistance, respectively. They share similarities not only in their sequences, but also in their target transcription binding sites. While CueR responds similarly to Au, Ag, or Cu to induce the expression of its target genes, GolS shows higher activation by Au than by Ag or Cu. We showed that the ability of GolS to distinguish Au from Cu resides in the metal-binding loop motif. Here, we identify the amino acids within the motif that determine in vivo metal selectivity. We show that residues at positions 113 and 118 within the metal-binding loop are the main contributors to metal selectivity. The presence of a Pro residue at position 113 favors the detection of Cu, while the presence of Pro at position 118 disfavors it. Our results highlight the molecular bases that allow these regulators to coordinate the correct metal ion directing the response to a particular metal injury.