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

A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR.

/pdf/crystallography-nmr-system-a-new-software-suite-for-50hlrhc0gc.pdf

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

The attraction of leukocytes to tissues is essential for inflammation and the host response to infection. The process is controlled by chemokines, which are chemotactic cytokines. This review introduces the burgeoning family of cytokines, with special emphasis on their role in the pathophysiology of disease and their potential as targets for therapy. Structure and Function of Chemokines Over 40 chemokines have been identified to date, most of them in the past few years. The relations among chemokines were not initially appreciated, which led to an idiosyncratic nomenclature consisting of many acronyms. When initially identified, these proteins had no known biologic . . .

Chemokines — Chemotactic Cytokines That Mediate Inflammation

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13Cα, 13Cβ, 13C′, 1Hα and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar φ and Ψ backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15°. Approximately 3% of the predictions made by TALOS are found to be in error.

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Protein backbone angle restraints from searching a database for chemical shift and sequence homology

https://spin.niddk.nih.gov/clore/Pub/pdf/355.pdf

The Xplor-NIH NMR molecular structure determination package.

https://spin.niddk.nih.gov/clore/Pub/pdf/381.pdf

Using Xplor-NIH for NMR molecular structure determination

The solution structure of the DNA binding domain of HIV-1 integrase (residues 220-270) has been determined by multidimensional NMR spectroscopy. The protein is a dimer in solution, and each subunit is composed of a five-stranded P-barrel with a topology very similar to that of the SH3 domain. The dimer is formed by a stacked @-interface comprising strands 2, 3, and 4, with the two triple-stranded antiparallel P-sheets, one from each subunit, oriented antiparallel to each other. One surface of the dimer, bounded by the loop between strands Pl and P2, forms a saddle-shaped groove with dimensions of approximately 24 x 23 x 12 8, in cross section. Lys264, which has been shown from mutational data to be involved in DNA binding, protrudes from this surface, implicating the saddle- shaped groove as the potential DNA binding site. The integrase protein of the human immunodeficiency virus (HIV) mediates a key step in the life cycle of the virus, namely the integration of a DNA copy of the viral genome into a host chromosome (see Goff, 1992; Vink & Plasterk, 1993; for reviews). HIV-1’ integrase is composed of three functional domains (Bushman et al., 1993; Engelman et al., 1993; van Gent et al., 1993; Vink et al., 1993): a small N-terminal domain that contains a His2Cys2 zinc binding motif, a central catalytic domain whose crystal structure has recently been solved (Dyda et al., 1994), and a C-terminal DNA binding domain. While the catalytic core domain can carry out a simple polynucleotidyl transfer termed disintegra- tion (Bushman et al., 1993), all three domains are required for the 3’ processing and DNA strand transfer activities that accomplish integration of the viral genome (Drelich et al., 1992; Schauer & Billich, 1992; Vink et al., 1993). Conse- quently, the N- and C-terminal domains provide additional potentially useful targets for rational drug design aimed at inhibiting HIV integration into the host genome. The function of the N-terminal domain is at present unknown, and in the case of the related Rous Sarcoma virus integrase at least, its integrity appears not to be essential for

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Solution structure of the DNA binding domain of HIV-1 integrase.

The three-dimensional structure of a member of the beta subfamily of chemokines, human macrophage inflammatory protein-1 beta (hMIP-1 beta), has been determined with the use of solution multidimensional heteronuclear magnetic resonance spectroscopy. Human MIP-1 beta is a symmetric homodimer with a relative molecular mass of approximately 16 kilodaltons. The structure of the hMIP-1 beta monomer is similar to that of the related alpha chemokine interleukin-8 (IL-8). However, the quaternary structures of the two proteins are entirely distinct, and the dimer interface is formed by a completely different set of residues. Whereas the IL-8 dimer is globular, the hMIP-1 beta dimer is elongated and cylindrical. This provides a rational explanation for the absence of cross-binding and reactivity between the alpha and beta chemokine subfamilies. Calculation of the solvation free energies of dimerization suggests that the formation and stabilization of the two different types of dimers arise from the burial of hydrophobic residues.

/pdf/high-resolution-solution-structure-of-the-beta-chemokine-4kk1jtqolq.pdf

High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR

NMR structures tend to be poorly packed and somewhat expanded relative to X-ray structures. 1 This is not a reflection of differences between the solution and crystal states, but rather of the nature of the experimental data and the computational methods employed to determine solution NMR structures. Indeed, the experimental NMR observables agree better with those calculated from high-resolution crystal structures than those calculated from the corresponding NMR structures. 2 NMR structures are mainly based on NOE-derived short interproton distance restraints which are generally classified into ranges. The NOE restraints determine the protein fold and pull the various structural elements into close spatial proximity, but the repulsive forces generated by the van der Waals term used to prevent atomic overlap tend to expand the structure. Because there are many more possible expanded structures than tightly packed ones that are compatible with the NOE data, the expansion can be regarded as an entropic effect. For globular proteins where there are numerous correlated NOE distance restraints and where the distance between structural elements is limited by covalent geometry, the problem of expansion may not be too severe, providing the structure is relatively well restrained by the NOE data. Intermolecular interfaces, on the other hand, will be particularly expanded since the density of intermolecular NOEs is usually limited and there are no intermolecular covalent restraints. Thus, there is a need for a structural restraint that can counteract the tendency toward expansion. In this paper, we demonstrate that the incorporation of a pseudopotential for the radius of gyration, Rgyr, a parameter that provides information regarding the global conformation of a molecule, can readily be incorporated into NMR structure calculations and results in significant increases in accuracy, particularly for protein-protein complexes. The Rgyr of a group of atoms is defined as the rms distance from each atom of the molecule to their centroid

/pdf/improving-the-packing-and-accuracy-of-nmr-structures-with-a-1qhzs09dmm.pdf

Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration

A new conformational database potential involving dihedral angle relationships in databases of high-resolution highly refined protein crystal structures is presented as a method for improving the quality of structures generated from NMR data. The rationale for this procedure is based on the observation that uncertainties in the description of the nonbonded contacts present a key limiting factor in the attainable accuracy of protein NMR structures and that the nonbonded interaction terms presently used have poor discriminatory power between high- and low-probability local conformations. The idea behind the conformational database potential is to restrict sampling during simulated annealing refinement to conformations that are likely to be energetically possible by effectively limiting the choices of dihedral angles to those that are known to be physically realizable. In this manner, the variability in the structures produced by this method is primarily a function of the experimental restraints, rather than an artifact of a poor nonbonded interaction model. We tested this approach with the experimental NMR data (comprising an average of about 30 restraints per residue and consisting of interproton distances, torsion angles, 3JHN alpha coupling constants, and 13C chemical shifts) used previously to calculate the solution structure of reduced human thioredoxin (Qin J, Clore GM, Gronenborn AM, 1994, Structure 2:503-522). Incorporation of the conformational database potential into the target function used for refinement (which also includes terms for the experimental restraints, covalent geometry, and nonbonded interactions in the form of either a repulsive, repulsive-attractive, or 6-12 Lennard-Jones potential) results in a significant improvement in various quantitative measures of quality (Ramachandran plot, side-chain torsion angles, overall packing). This is achieved without compromising the agreement with the experimental restraints and the deviations from idealized covalent geometry that remain within experimental error, and the agreement between calculated and observed 1H chemical shifts that provides an independent NMR parameter of accuracy. The method is equally applicable to crystallographic refinement, and should be particular useful during the early stages of either an NMR or crystallographic structure determination and in cases where relatively few experimental restraints can be derived from the measured data (due, for example, to broad lines in the NMR spectra or to poorly diffracting crystals).

https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.5560050609

John Kuszewski

Papers

Using Xplor-NIH for NMR molecular structure determination

Solution structure of the DNA binding domain of HIV-1 integrase.

High-resolution solution structure of the beta chemokine hMIP-1 beta by multidimensional NMR

Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration

Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases