抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over-stabilization of alpha-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "Amber" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone phi/psi dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the phi/psi dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems.

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Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Infrared spectroscopy of proteins.

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.

Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study.

UV resonance Raman studies of peptide and protein secondary structure demonstrate an extraordinary sensitivity of the amide III (Am III) vibration and the CαH bending vibration to the amide backbone conformation. We demonstrate that this sensitivity results from a Ramachandran dihedral ψ angle dependent coupling of the amide N−H motion to (C)CαH motion, which results in a ψ dependent mixing of the Am III and the (C)CαH bending motions. The vibrations are intimately mixed at ψ ∼ 120°, which is associated with both the β-sheet conformation and random coil conformations. In contrast, these motions are essentially unmixed for the α-helix conformation where ψ ∼ −60°. Theoretical calculations demonstrate a sinusoidal dependence of this mixing on the ψ angle and a linear dependence on the distance separating the N−H and (C)CαH hydrogens. Our results explain the Am III frequency dependence on conformation as well as the resonance Raman enhancement mechanism for the (C)CαH bending UV Raman band. These results may ...

Dihedral ψ Angle Dependence of the Amide III Vibration: A Uniquely Sensitive UV Resonance Raman Secondary Structural Probe

Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure A critical review

In their reVised Comment,1 Jordan and Spiro (JS) take issue with our recent assessments2,3 of their interpretations4-6 of the nature and the resonance Raman enhancement of two bands of aqueous N-methylacetamide (NMA), viz., the ∼1380 cm-1 CCH3 symmetric bend (sb) and the amide I normal modes. In this reVised Reply, we respond in turn to the two specific points raised in their Comment. 1. Enhancement Mechanism of Amide S. The enhancement of the ∼1380 cm-1 CCH3 sb mode has two aspects that need consideration: the nature of this mode and the origin of its enhancement. We note first that there is no question that this mode in aqueous NMA is predominantly CCH3 sb with a significant contribution of CCH3 antisymmetric bend7 and a small contribution of CC stretch (s).2,8 Therefore, it is not only desirable, as is common practice, that it should be referred to by its major contributing local symmetry coordinate but it is also inappropriate to refer to it as an “amide” mode, which historically9 has been reserved for characteristic normal modes of the CONH group. The amide S designation4 should be dropped. With respect to the enhancement mechanism of this mode, Spiro et al.4-6 have stated that it arises from vibrational mixing with the nearby amide III mode. We have taken exception to this explanation,2 on grounds of both its formulation and its factual basis. We start out with the belief that there is merit in precise formulations of concepts. To imply that there is vibrational mixing between normal coordinates4-6 is indeed “inaccurate”.1,2 In their revised Comment, JS state that they “meant the sharing of internal coordinates between normal modes of similar energy”. While this is closer to the truth, in that a given internal coordinate can contribute to different normal modes, we note that these need not be of “similar energy”: for example, in aqueous NMA8 the CCN deformation coordinate makes small contributions to amide I at 1626 cm-1 and to the CN s mode at 883 cm-1 while its major contribution is to the normal mode at 446 cm-1. With respect to the origin of the enhancement of the CCH3 sb mode, this has been said to be “dependent primarily on the C-N displacement in the excited state” 4 and due to “vibrational mixing between the CN stretch of amide III and (C)CR hydrogen bending displacements”.6 In fact, CN s makes a negligible contribution to the potential energy distribution of the CCH sb mode,7,8 and in terms of the eigenvector components of the enhancement,3 CC s is 60% larger than CN s.10 That the CC s contribution is the crucial one is evidenced by “The lack of resonance enhancement for CCH3sb in [NMA-ND, which] is caused by the reduction and the sign change of the CC s contribution.” 2 It is, thus, clear that CN s, which is a dominant component of amide III, does not play the major role in the resonance Raman enhancement of the CCH3sb mode. In their revised Comment, JS “do not contest” our analysis. 2. Enhancement Mechanism of Amide I. There is a fundamental disagreement between Spiro et al. and our group concerning the origin of the resonance Raman enhancement of the amide vibrations, especially the amide I vibration. These conflicting views result in different conclusions concerning the nature of the amide ππ* excited state and also in different conclusions about the excited state geometry differences between NMA in aqueous solution versus that in non-hydrogen-bonding solvents and in the gas phase. The correct interpretation is needed in order to develop a deep understanding of amide electronic and vibrational spectroscopy and to utilize UV resonance Raman spectroscopy for protein secondary structural investigations. The disagreement is summarized succinctly: Spiro et al. claim that their experimental data for NMA in aqueous solution, in either H2O or D2O, indicate that amide I enhancement does not arise from the lowest energy amide ππ* excited state, which gives rise to the absorption band at ca. 190 nm, even when excitation occurs directly within this absorption band. In contrast, we claim that the previous experimental data simply and directly force the conclusion that the amide I band is resonance enhanced by this ππ* excited state. The ability to reconcile these views was previously clouded by disagreement over the experimental excitation profile results for NMA in H2O and D2O. Although our preresonance excitation profile data above 220 nm3 were similar to those of Wang et al.,5 their Raman cross sections were ca. 2-fold larger than ours for excitation within the amide π f π* transition (below 200 nm). This disagreement has now been reconciled, and JS now concede that their data were not corrected for the π f π* transition self-absorption. Our excitation profile data3 demonstrated that in the region between 192 and 220 nm the amide I Raman cross sections are relatively constant compared to the amide II and III cross sections. In fact, we directly plotted the amide I′/amide II′ ratio in the region between 192 and 235 nm and found the ratio to be essentially constant. JS have now similarly found that the amide I′/amide II′ as well as amide I/amide II intensity ratios are constant in this region. Both groups agree that the amide II and III bands are enhanced dominantly by the 190 nm ππ* excited state. The constant ratio between the amide I and amide II Raman cross sections indicates that these bands have the same frequency dispersion over the region excited; thus, we simply concluded that the amide I and I′ bands are enhanced by the 190 nm ππ* excited state. Any other conclusion requires that the dispersions fortuitously coincide. Spiro et al. continue to argue that the second π f π* transition at ∼165 nm is the only source of enhancement of the amide I band.4 We argued that it is impossible for the preresonance Raman dispersion of amide I from a ca. 165 nm transition to show the same dispersion as the amide II band, which is only enhanced by the 190 nm π f π* transition. In † Permanent address: University of Bremen, FBI-Institute of Experimental Physics, 28359 Bremen, Germany. * To whom correspondence should be addressed. 3992 J. Phys. Chem. A 1997, 101, 3992-3994

Vibrational assignments of trans-n-methylacetamide and some of its deuterated isotopomers from band decomposition of ir, visible, and resonance raman spectra

Determination of the precise solution structure of peptides is of utmost importance to the understanding of protein folding and peptide drugs. Herein, we have measured the UV circular dichroism (UVCD) spectra of tri-alanine dissolved in D(2)O, H(2)O, and glycerol. The results clearly show the coexistence of a polyproline II or 3(1)-helix and a somewhat disordered flat beta-strand conformation, in complete agreement with recent predictions from spectroscopic data (Eker et al. J. Am. Chem. Soc. 2002, 124, 14 330-14 341). A thermodynamic analysis revealed that enthalpic contributions of about 11 and 17 kJ/mol stabilize polyproline II in D(2)O and H(2)O, respectively, but at room temperature they are counterbalanced by entropic contributions, which clearly favor the more disordered beta-strand conformation. It is hypothesized that this delicate balance is the reason for the variety of structural propensities of amino acid residues in the absence of nonlocal interactions. The isotope effect yielding a higher occupation of polyproline II in H(2)O with respect to D(2)O strongly suggests that a hydrogen-bonding network involving the peptide and water molecules in the hydration shell plays a major role in stabilizing this conformation. The equilibrium between polyproline II and beta-strand is practically maintained in glycerol, which suggests that glycerol can substitute water as stabilizing solvent for the polyproline II conformation. We also measured the UVCD spectra of tri-valine and tri-lysine (both at acidic pD) in D(2)O and found them to adopt a flat beta-strand and left-handed turn structure, respectively, in accordance with recent analyses of vibrational spectroscopy data. Generally, the present study adds substantial evidence to the notion that the so-called random coil state of peptides is much more structured than generally assumed.

Reinhard Schweitzer-Stenner

Papers

Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study.

Dihedral ψ Angle Dependence of the Amide III Vibration: A Uniquely Sensitive UV Resonance Raman Secondary Structural Probe

Advances in vibrational spectroscopy as a sensitive probe of peptide and protein structure A critical review

Vibrational assignments of trans-n-methylacetamide and some of its deuterated isotopomers from band decomposition of ir, visible, and resonance raman spectra

Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy.