Fluorinated Aromatic Amino Acids Distinguish Cation-π Interactions from Membrane Insertion

Cation-π interactions, where protein aromatic residues supply π systems while a positive-charged portion of phospholipid head groups are the cations, have been suggested as important binding modes for peripheral membrane proteins. However, aromatic amino acids can also insert into membranes and hydrophobically interact with lipid tails. Heretofore there has been no facile way to differentiate these two types of interactions. We show that specific incorporation of fluorinated amino acids into proteins can experimentally distinguish cation-π interactions from membrane insertion of the aromatic side chains. Fluorinated aromatic amino acids destabilize the cation-π interactions by altering electrostatics of the aromatic ring, whereas their increased hydrophobicity enhances membrane insertion. Incorporation of pentafluorophenylalanine or difluorotyrosine into a Staphylococcus aureus phosphatidylinositol-specific phospholipase C variant engineered to contain a specific PC-binding site demonstrates the effectiveness of this methodology. Applying this methodology to the plethora of tyrosine residues in Bacillus thuringiensis phosphatidylinositol-specific phospholipase C definitively identifies those involved in cation-π interactions with phosphatidylcholine. This powerful method can easily be used to determine the roles of aromatic residues in other peripheral membrane proteins and in integral membrane proteins.     

How to Synthesize A tRNA?

Abstract

New blocking group combinations have been investigated to achieve an automated synthesis of a tRNA and structural analogs on solid-support. The use of the 4-methoxytetrahydropyranyl group for 2′-OH-protection and the dansylethoxycarbonyl group for the 5′-OH position shows in the phosphoramidite approach good results. In the arabino series the 2-(4-nitrophenyl)ethoxycarbonyl group is a perfect 2′-OH blocking group which can be combined with the dimethoxytrityl residue in the usual manner to give high yields and pure materials.     

Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using ?-Amino Acids

Chirality plays a major role in recognition and interaction of biologically important molecules. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) is the first enzyme of the shikimate pathway, which is responsible for the synthesis of aromatic amino acids in bacteria and plants, and a potential target for the development of antibiotics and herbicides. DAH7PS from Mycobacterium tuberculosis (MtuDAH7PS) displays an unprecedented complexity of allosteric regulation, with three interdependent allosteric binding sites and a ternary allosteric response to combinations of the aromatic amino acids l-Trp, l-Phe and l-Tyr. In order to further investigate the intricacies of this system and identify key residues in the allosteric network of MtuDAH7PS, we studied the interaction of MtuDAH7PS with aromatic amino acids that bear the non-natural d-configuration, and showed that the d-amino acids do not elicit an allosteric response. We investigated the binding mode of d-amino acids using X-ray crystallography, site directed mutagenesis and isothermal titration calorimetry. Key differences in the binding mode were identified: in the Phe site, a hydrogen bond between the amino group of the allosteric ligands to the side chain of Asn175 is not established due to the inverted configuration of the ligands. In the Trp site, d-Trp forms no interaction with the main chain carbonyl group of Thr240 and less favourable interactions with Asn237 when compared to the l-Trp binding mode. Investigation of the MtuDAH7PS_N175A variant further supports the hypothesis that the lack of key interactions in the binding mode of the aromatic d-amino acids are responsible for the absence of an allosteric response, which gives further insight into which residues of MtuDAH7PS play a key role in the transduction of the allosteric signal.     

How Do Rituals Affect Cooperation?

Collective rituals have long puzzled anthropologists, yet little is known about how rituals affect participants. Our study investigated the effects of nine naturally occurring rituals on prosociality. We operationalized prosociality as (1) attitudes about fellow ritual participants and (2) decisions in a public goods game. The nine rituals varied in levels of synchrony and levels of sacred attribution. We found that rituals with synchronous body movements were more likely to enhance prosocial attitudes. We also found that rituals judged to be sacred were associated with the largest contributions in the public goods game. Path analysis favored a model in which sacred values mediate the effects of synchronous movements on prosocial behaviors. Our analysis offers the first quantitative evidence for the long-standing anthropological conjecture that rituals orchestrate body motions and sacred values to support prosociality. Our analysis, moreover, adds precision to this old conjecture with evidence of a specific mechanism: ritual synchrony increases perceptions of oneness with others, which increases sacred values to intensify prosocial behaviors.     

Constitutional Amino Acids of the Antibiotic YA–56

Acid hydrolysis of the antibiotic YA-56 X (Zorbamycin) and Y belonging to the phleomycin-bleomycin group was carried out and the following constitutional amino acids were isolated from the hydrolyzate of YA–56 X: β-Amino-β-(4-amino-6-carboxy-5-methylpyrimidine-2-yl)- propionic acid, β-aminoalanine, L-erythro-β-hydroxyhistidine and 3 unidentified amino acids. Though the former 3 amino acids were known to be constituents of phleomycins and bleomycins, the latter three were not found in phleomycins and bleomycins. YA–56 Y gave one more unidentified amino acid.

Furthermore, isolation of β-alanine and 2-acetylthiazole-4-carboxylic acid from the hydrolyzate indicated the presence of 2-(2-(2-aminoethyl)-Δ²-thiazoline-4-yl)-thiazole-4-carboxylic acid in YA–56 X and Y as in phleomycins.     

Studies on γ-Radiolysis of Sulfur Containing Amino Acids

In connection with flavor deterioration accompanied by food irradiation, the effect of γ-irradiation on sulfoxide amino acids in air free aqueous system was investigated. The major radiolysis products from S-n-propyl-l-cysteine sulfoxide (PCSO) were alanine, cysteic acid, dipropyl disulfide, etc., and from S-allyl-l-cysteine sulfoxide (ACSO) were S-allyl-l-cysteine, cystine, cysteic acid, etc., which were isolated chromatographycally and identified by using IR and mass spectrometry. The sulfoxide in ACSO was more easily reduced to sulfide than that of in PCSO, and the bond of S-C (β-carbon in alanine moiety) in ACSO was difficult to cleave. These differences observed between PCSO and ACSO in the radiolysis products and their yields indicate that the radiolysis degradation is considerably influenced by the structure of alkyl group. From the experiments with N₂O or KBr addition during irradiation, principal roles of the active species in irradiated water in the degradation processes were partly elucidated.     

Pyrolysis of β-Hydroxy Amino Acids,Especially l-Serine

From the pyrolysis of l-serine, ten volatile compounds including several pyrazines were identified. Pyrazines were also found from the pyrolysis of l-threonine, but not from that of alanine and considered to be characteristic pyrolysis products of β-hydroxy amino acids. At the same time, diketopiperazines, amines and carbonyl compounds were also found in addition to those described above. Formation mechanism of pyrazine compounds was also discussed.     

Cell Penetrating Peptides: How Do They Do It?

Cell penetrating peptides consist of short sequences of amino acids containing a large net positive charge that are able to penetrate almost any cell, carrying with them relatively large cargoes such as proteins, oligonucleotides, and drugs. During the 10 years since their discovery, the question of how they manage to translocate across the membrane has remained unanswered. The main discussion has been centered on whether they follow an energy-independent or an energy-dependent pathway. Recently, we have discovered the possibility of an energy-independent pathway that challenges fundamental concepts associated with protein-membrane interactions (Herce and Garcia, PNAS, 104: 20805 (2007) [1]). It involves the translocation of charged residues across the hydrophobic core of the membrane and the passive diffusion of these highly charged peptides across the membrane through the formation of aqueous toroidal pores. The aim of this review is to discuss the details of the mechanism and interpret some experimental results consistent with this view.     

How Do Children Solve Aesop's Fable?

Studies on members of the crow family using the "Aesop's Fable" paradigm have revealed remarkable abilities in these birds, and suggested a mechanism by which associative learning and folk physics may interact when learning new problems. In the present study, children between 4 and 10 years of age were tested on the same tasks as the birds. Overall the performance of the children between 5-7-years was similar to that of the birds, while children from 8-years were able to succeed in all tasks from the first trial. However the pattern of performance across tasks suggested that different learning mechanisms might be being employed by children than by adult birds. Specifically, it is possible that in children, unlike corvids, performance is not affected by counter-intuitive mechanism cues.     

How Do Kinetochores CLASP Dynamic Microtubules?

Maintenance of genetic stability during cell division requires binding of chromosomes to the mitotic spindle, a process that involves attachment of spindle microtubules to kinetochores. This enables chromosomes to move to the metaphase plate, to satisfy the spindle checkpoint and finally to segregate during anaphase. Recent studies on the function MAST in Drosophila and its human homologue CLASP1, have revealed that these microtubule-associated proteins play an essential role for the kinetochore-microtubule interaction. CLASP1 localizesto the plus ends of growing microtubules and to the most external kinetochore domain. Depletion of CLASP1 causes abnormal chromosome congression, collapse of the mitotic spindle and attachment of kinetochores to very short microtubules that do not show dynamic behavior. These results suggest that CLASP1 is required at kinetochores to regulate the dynamic behavior of attached microtubules.     

β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides

Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that β-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.     

How Old is Earth,and How Do We Know?

Earth scientists have devised many complementary and consistent techniques to estimate the ages of geologic events. Annually deposited layers of sediments or ice document hundreds of thousands of years of continuous Earth history. Gradual rates of mountain building, erosion of mountains, and the motions of tectonic plates imply hundreds of millions of years of change. Radiometric dating, which relies on the predictable decay of radioactive isotopes of carbon, uranium, potassium, and other elements, provides accurate age estimates for events back to the formation of Earth more than 4.5 billion years ago. These and other dating techniques are mutually consistent and underscore the reality of “deep time” in Earth history.