Investigation into the ROMP copolymerization of peptide‐ and PEG‐functionalized norbornene derivatives

The ring‐opening metathesis polymerizations (ROMP), using RuCl₂ (PCy₃)₂CHPh, of a series of peptide‐functionalized norbornene derivatives have been investigated. Incorporation of a PEG‐monomer was found to prevent premature precipitation of polymer strands during the course of polymerization reactions and yield water compatible polymers in high conversions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 3178–3190, 2007     

Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

Foaming and Structural Studies on the Acidic Subunit of Amaranth 11S Globulin Modified with Antihypertensive Peptides as a Function of pH and Ionic Strength

Some studies aimed at revealing the relationship between protein structure and their functional properties. However, the majority of these reports have been carried out using protein isolates. There are limited reports on the possible relationship between the functional properties and the structure of a purified protein. In this work the amaranth 11S globulin acidic subunit (AAC) and five mutations of the same protein that were modified in their variable regions with antihypertensive peptides (VYVYVYVY and RIPP), were analyzed at two ionic strength (2.9 and 17.6 g/L NaCl) and pH (3.0–7.0). Results revealed better solubility for the proteins mutated at the terminal ends (AACM.1 and AACM.4) and lower solubility for the protein inserted with RIPP peptide. Spectroscopy studies revealed an increase of β-sheet structure at high salt concentration for all proteins. It was also observed that salt concentration acted as a modulator, which allowed a better foam features for all modified proteins limiting movement of side chains and reducing red-shifted displacement of λmax. All proteins showed foam capacity ranging from 76 to 93% although foam stability was twofold better for modified proteins than for AAC at high salt concentration. This study allowed better understanding about the structural changes that influence the foaming properties of engineered proteins.     

A Testable Theory for the Emergence of the Classical World

The transition from the quantum to the classical world is not yet understood. Here, we take a new approach. Central to this is the understanding that measurement and actualization cannot occur except on some specific basis. However, we have no established theory for the emergence of a specific basis. Our framework entails the following: (i) Sets of N entangled quantum variables can mutually actualize one another. (ii) Such actualization must occur in only one of the 2^N possible bases. (iii) Mutual actualization progressively breaks symmetry among the 2^N bases. (iv) An emerging “amplitude” for any basis can be amplified by further measurements in that basis, and it can decay between measurements. (v) The emergence of any basis is driven by mutual measurements among the N variables and decoherence with the environment. Quantum Zeno interactions among the N variables mediates the mutual measurements. (vi) As the number of variables, N, increases, the number of Quantum Zeno mediated measurements among the N variables increases. We note that decoherence alone does not yield a specific basis. (vii) Quantum ordered, quantum critical, and quantum chaotic peptides that decohere at nanosecond versus femtosecond time scales can be used as test objects. (viii) By varying the number of amino acids, N, and the use of quantum ordered, critical, or chaotic peptides, the ratio of decoherence to Quantum Zeno effects can be tuned. This enables new means to probe the emergence of one among a set of initially entangled bases via weak measurements after preparing the system in a mixed basis condition. (ix) Use of the three stable isotopes of carbon, oxygen, and nitrogen and the five stable isotopes of sulfur allows any ten atoms in the test protein to be discriminably labeled and the basis of emergence for those labeled atoms can be detected by weak measurements. We present an initial mathematical framework for this theory, and we propose experiments.     

Fluorescence studies on the conformation of litorin in solution and in the presence of model membranes

The conformation of the nonapeptide hormone litorin has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence. The results obtained show that, in buffer, the hormone probably exists in a collection of flexible conformers, slowly interconverting between them. The marked changes observed in fluorescence spectra and lifetimes upon addition of dimyristoylphosphatidylserine vesicles clearly show that the peptide interacts with lipids assuming lipid specific conformations. Interestingly, no significative spectroscopic changes are produced by exposure to dimirystoylphosphatidylcholine vesicles both in the gel and liquid-christalline phases, suggesting a requirement for negatively charged lipids during the process of hormone-membrane interaction.     

IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Fluorescent Temporin B Derivative and its Binding to Liposomes

Temporins are short (10–13 amino acids) and linear antimicrobial peptides first isolated from the skin of the European red frog, Rana temporaria, and are effective against Gram-positive bacteria and Candida albicans. Similarly to other antimicrobial peptides, the association of temporins to lipid membranes has been concluded to underlie their antimicrobial effects. Accordingly, a detailed understanding of their interactions with phospholipids is needed. We conjugated a fluorophore (Texas Red) to a Cys containing derivative of temporin B (temB) and investigated its binding to liposomes by fluorescence spectroscopy. Circular dichroic spectra for the Cys-mutant recorded in the absence and in the presence of phospholipids were essentially similar to those for temB. A blue shift in the emission spectra and diminished quenching by ferrocyanide (FCN) of Texas Red labeled temporin B (TRC-temB) were seen in the presence of liposomes. Both of these changes can be attributed to the insertion of the Texas Red into the hydrophobic region of the bilayer. Resonance energy transfer, steady state anisotropy, and fluorescence lifetimes further demonstrate the interaction of TRC-temB with liposomes to be enhanced by negatively charged phospholipids. Instead, cholesterol attenuates the association of TRC-temB with membranes. The interactions between TRC-temB and liposomes of varying negative surface charge are driven by electrostatics as well as hydrophobicity. Similarly to native temporin B also TRC-temB forms amyloid type fibers in the presence of negatively charged liposomes. This property is likely to relate to the cytotoxic activity of this peptide.     

Vibrational spectra and crystal structure of the di‐amino acid peptide cyclo(L‐Met‐L‐Met): comparison of experimental data and DFT calculations

Experimental Raman and FT‐IR spectra of solid‐state non‐deuterated and N‐deuterated samples of cyclo(L ‐Met‐L ‐Met) are reported and discussed. The Raman and FT‐IR results show characteristic amide I vibrations (Raman: 1649 cm⁻¹, infrared: 1675 cm⁻¹) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at ∼1493 cm⁻¹ but no IR band is observed in this region. Cyclo(L ‐Met‐L ‐Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3‐LYP/cc‐pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X‐ray structure. Copyright © 2009 John Wiley & Sons, Ltd.     

中等规模多肽分子的2DNOESY实验问题

由于中等规模多肽在水溶液中运动的特殊性(ω₀τ_c≈1),2DNOESY谱上往往得不到相关讯息(采用合理的混合时间),而降低温度的余地也很小·本工作将少量氘代甲醇加到水溶液中,并将实验温度降到零下,实验取得成功。例如从一个九肽和一个十一肽的NOESY实验得到了很多残基内和残基间的NOESY相关讯息,足以作出归属并进一步计算质子间距离.     

(KN3)n(n=1~5)团簇结构与性质的密度泛函理论研究

利用密度泛函理论B3LYP方法, 在6-311G*基组水平上对(KN3)n(n=1~5)团簇各种可能的结构进行了几何结构优化, 预测了各团簇的最稳定结构. 并对最稳定结构的振动特性、成键特性、电荷分布和稳定性性质进行了分析研究. 结果表明, 叠氮化合物中叠氮基以直线型存在, KN3团簇最稳定结构为直线型, (KN3)n(n=2~3)团簇最稳定结构为环形结构, (KN3)n(n=4~5)团簇最稳定结构是由(KN3)2团簇最稳定结构形成的平面和空间结构. N-N 键键长在0.1156~0.1196 nm之间, N-K键键长在0.2357~0.2927 nm之间; 叠氮基中间的N原子显示正电性, 两端的N原子显示负电性, 且与K原子直接作用的N原子负电性更强, 金属K原子与N原子之间形成离子键. (KN3)n(n=1~5)团簇最稳定结构的IR光谱最强振动峰均位于2180~2230 cm-1, 振动模式为叠氮基中N-N键的反对称伸缩振动. 稳定性分析显示, (KN3)3团簇具有相对较高的动力学稳定性.