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

I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

Molecular recognition is central to all biological processes. For the past 50 years, Koshland's 'induced fit' hypothesis has been the textbook explanation for molecular recognition events. However, recent experimental evidence supports an alternative mechanism. 'Conformational selection' postulates that all protein conformations pre-exist, and the ligand selects the most favored conformation. Following binding the ensemble undergoes a population shift, redistributing the conformational states. Both conformational selection and induced fit appear to play roles. Following binding by a primary conformational selection event, optimization of side chain and backbone interactions is likely to proceed by an induced fit mechanism. Conformational selection has been observed for protein-ligand, protein-protein, protein-DNA, protein-RNA and RNA-ligand interactions. These data support a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact our views and strategies in drug design, biomolecular engineering and molecular evolution.

/pdf/the-role-of-dynamic-conformational-ensembles-in-biomolecular-33rwd16x5b.pdf

The role of dynamic conformational ensembles in biomolecular recognition

The synergy between structure and dynamics is essential to the function of biological macromolecules. Thermally driven dynamics on different timescales have been experimentally observed or simulated, and a direct link between micro- to milli-second domain motions and enzymatic function has been established. However, very little is understood about the connection of these functionally relevant, collective movements with local atomic fluctuations, which are much faster. Here we show that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state. The fast, local mobilities differ between a mesophilic and hyperthermophilic adenylate kinase, but are strikingly similar at temperatures at which enzymatic activity and free energy of folding are matched. The connection between different timescales and the corresponding amplitudes of motions in adenylate kinase and their linkage to catalytic function is likely to be a general characteristic of protein energy landscapes.

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.

A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss)Bonnet theorem. The surface routine was implemented in FANTOM, a program for energy minimization and Monte Carlo simulation, and tested for accuracy and efficiency in extensive energy minimizations of Met-enkephalin, the a-amylase inhibitor . tendamistat, and avian pancreatic polypeptide APP . The CPU time for the exact calculation of the accessible surface areas and their gradients has been . . reduced by factors of 2.2 Met-enkephalin and 3.2 tendamistat compared with our previous approach. The efficiency of our exact method is similar to the recently described approximate methods MSEED and SASAD. The performance of several atomic solvation parameter sets was tested in searches for low energy conformations of APP among conformations near the native X-ray crystal structure and highly distorted structures. The protein solvation parameters from w . x

Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules

Analysis of protein-lipid interactions based on model simulations of electron spin resonance spectra

The focus of structural biology is on studies of the highly populated, ground states of biological molecules; states that are only sparsely and transiently populated are more difficult to probe because they are invisible to most structural methods. Yet, such states can play critical roles in biochemical processes such as ligand binding, enzyme catalysis, and protein folding. A description of these states in terms of structure and dynamics is, therefore, of great importance. Here, we present a method, based on relaxation dispersion NMR spectroscopy of weakly aligned molecules in a magnetic field, that can provide such a description by direct measurement of backbone amide bond vector orientations in transient, low populated states that are not observable directly. Such information, obtained through the measurement of residual dipolar couplings, has until now been restricted to proteins that produce observable spectra. The methodology is applied and validated in a study of the binding of a target peptide to an SH3 domain from the yeast protein Abp1p and subsequently used in an application to protein folding of a mutational variant of the Fyn SH3 domain where 1H-15N dipolar couplings of the invisible unfolded state of the domain are obtained. The approach, which can be used to obtain orientational restraints at other sites in proteins as well, promises to significantly extend the available information necessary for providing a site-specific characterization of structural properties of transient, low populated states that have to this point remained recalcitrant to detailed analysis.

https://www.pnas.org/content/pnas/104/47/18473.full.pdf

Measurement of bond vector orientations in invisible excited states of proteins

We report on careful line shape studies of slow motional and orientation dependent ESR spectra of a deuterated liquid‐crystal‐like spin probe dissolved in a benzilidene‐derivative (40,6) and in cyanobiphenyl derivative (S2 and 5CB) liquid crystals. The simulation of the ESR spectra is based on the Lanczos algorithm recently applied by Moro and Freed in a general and efficient formulation of slow motional and ordering effects on ESR line shapes. With 40,6 which exhibits monolayer smectic phases, we find that the main change in the spin relaxation upon passing from the nematic to the smectic A phase consists of changes occuring in ordering attributable to packing forces on functional groups. Such ordering effects appear to be further enhanced in the SB phase with consequent alterations in dynamics. With S2, which exhibits an interpenetrating bilayer smectic A phase, we find unusual ESR spectra in that phase which may be simulated on the basis of a model of cooperative distortions static on the ESR time scale, and superimposed on individual molecular reorientation. This mode is interpreted as a collective chain distortion which affects the orientational distribution of the piperidine ring of the spin probe. A similar phenomenon is observed in the supercooled nematic phase of 5CB, which is aligned by an electric field, and evidence is also found that the reorientational dynamics of this ring are affected by interaction with local cooperative modes in the liquid crystal (i.e., a SRLS mechanism previously proposed by Freed and co‐workers). Some microscopic characteristics of liquid crystals revealed by this and previous ESR spin probe studies are discussed.

Electron‐spin relaxation and ordering in smectic and supercooled nematic liquid crystals

The two-body Slowly Relaxing Local Structure (SRLS) model was applied to 15N NMR spin relaxation in proteins and compared with the commonly used original and extended model-free (MF) approaches. In MF, the dynamic modes are assumed to be decoupled, local ordering at the N−H sites is represented by generalized order parameters, and internal motions are described by effective correlation times. SRLS accounts for dynamical coupling between the global diffusion of the protein and the internal motion of the N−H bond vector. The local ordering associated with the coupling potential and the internal N−H diffusion are tensors with orientations that may be tilted relative to the global diffusion and magnetic frames. SRLS generates spectral density functions that differ from the MF formulas. The MF spectral densities can be regarded as limiting cases of the SRLS spectral density. SRLS-based model-fitting and model-selection schemes similar to the currently used MF-based ones were devised, and a correspondence betwe...

A structural mode-coupling approach to 15N NMR relaxation in proteins.

Deuterium NMR spectra of polycrystalline (tyrosine-3,5-*H2) (Leus)enkephalin show that the aromatic tyrosyl ring of this pentapeptide is executing 180' flips about the Cfl-C' axis in the solid state. Specifically, the axially symmetric powder pattern observed at low temperature collapses to an axially asymmetric pattern with TJ 0.6 at high temperature. Computer simulations of the NMR line shapes, which account for spectral distortions induced by the quadrupole echo technique, indicate that at room temperature the flipping rate is approximately 5 X IO4 s-* and that it increases to about lo6 s-I at 101 "C. In the past few years it has become apparent that solid-state NMR spectra can be employed to investigate the rate and mechanism of molecular reorientation processes in solids, and there are now several examples in the literature which demonstrate this point."" To date these studies have focussed on small crystalline molecules, but the techniques are equally applicable to large molecules such as peptides and proteins, where they can be used to obtain information on phenomena such as the motion of amino acid side chains. As part of a study of side-chain reorientation in peptides and proteins by solid-state NMR, we report here an investigation of the motion of the aromatic tyrosine ring in polycrystalline (Le~~jenkephalin. Specifically, the 2H NMR powder line shapes of ( tyrosine-3 ,S2H2) ( LeuS) enkephalin show that the tyrosyl group is not rigid, but instead is executing jumps of 180' about the Co-Cc axis of the aromatic ring. At room temperature the jump rate is approximately lo4 s-l and inceases to about IO6 s-' at 101 OC. (Le~~lenkephalin is a natural pentapeptide with the sequence Tyr-Gly-Gly-Phe-Leu which has been chemically labeled with (3,5-ZH2)tyrosine for this study as is depicted in Figure 1. The peptide is of considerable interest because of its structural similarity to opiate agonists. Theoretical and experimental evidence from solution measurementsl2 reveal that enkephalin may exist in a relatively rigid conformation in which the phenyl and tyrosyl rings are separated by a distance similar to that of opiates, so that these groups may participate in binding to the receptor. (Leus)enke- phalin has been crystallized, and its structure determined;l3-l5 the X-ray studies have suggested that the orientation of the tyrosyl side chain is not unique, the ring experiencing disorder of either a static or dynamic nature. Because of the possible existence of dynamic disorder, and because NMR can detect this type of disorder and reveal the details of its nature, a solid-state NMR investigation of (Leus)enkephalin appeared promising. Experimental Section ~~-(3,5-2H,)Tyrosine was purchased from Merck, Sharpe, and Dohme (St. Louis, Mo.). The DL form was resolved by treatment of the N-trifluoroacetyl derivative with carboxypeptidase A to yield the L isomer of the free amino acid. The latter was used to synthesize (Leus)enke- phalin by the procedure reported previously.12 The 2H labeled peptide was recrystallized from ethanol. Samples for the NMR experiments typically consisted of approxi- mately 50 mg of the 2H-labeled peptide and were placed in vacuum- sealed glass tubes. The ZH NMR spectra were obtained on a home-built spectrometer operating at 45.1 MHz for 2H, using a quadrupole echo pulse seq~encc.'~~'~ The r/2 pulse width was 2-2.5 ps and the T value in the echo experiment was 30 ps. In order to ensure that the line shapes we obtain are accurate, we have found it necessary to employ quadrature, rather than single sided, phase detection. With the latter method gross

/pdf/rotational-jumps-of-the-tyrosine-side-chain-in-crystalline-2djdmdxgto.pdf

Eva Meirovitch

Papers

Analysis of protein-lipid interactions based on model simulations of electron spin resonance spectra

Measurement of bond vector orientations in invisible excited states of proteins

Electron‐spin relaxation and ordering in smectic and supercooled nematic liquid crystals

A structural mode-coupling approach to 15N NMR relaxation in proteins.

Rotational jumps of the tyrosine side chain in crystalline enkephalin. Hydrogen-2 NMR line shapes for aromatic ring motions in solids