Molecular dynamics simulation on HP1 protein binding by histone H3 tail methylation and phosphorylation

Trimethylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging, and heterochromatin formation. Phosphorylation of histone H3 has been linked with mitotic chromatin condensation. During mitosis in vivo, H3 lysine 9 methylation and serine 10 phosphorylation can occur concomitantly on the same histone tail, whereas the influence of phosphorylation to trimethylation H3 tail recruiting HP1 remains controversial. In this work, molecular dynamics simulation of HP1 complexed with both trimethylated and phosphorylated H3 tail were performed and compared with the results from the previous methylated H3‐HP1 trajectory. It is clear from the 10‐ns dynamics simulation that two adjacent posttranslational modifications directly increase the flexibility of the H3 tail and weaken HP1 binding to chromatin. A combinatorial readout of two adjacent posttranslational modifications—a stable methylation and a dynamic phosphorylation mark—establish a regulatory mechanism of protein–protein interactions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

组蛋白H3赖氨酸27和36位甲基化修饰的鉴定

采用液相色谱-质谱联用技术结合生物信息学分析手段,研究Hela细胞组蛋白H3赖氨酸(Lysine (K))K27和K36位点带有甲基化和二甲基化修饰的多肽鉴定,通过二级质谱碎片解析和二级碎片丰度分析,对组蛋白H3赖氨酸K27和K36上甲基化和二甲基化修饰进行了鉴定和分析。     

基于ProteinGoggle 2.0的组蛋白H4蛋白质变体的自上而下表征

由于大量可能蛋白质变体以及每一个翻译后修饰大量可能位点的存在,核心组蛋白上密集的组合式翻译后修饰的自上而下表征一直是一个巨大的分析挑战。结合高分辨串级质谱,基于同位素质荷比和轮廓指纹比对的整体蛋白质数据库搜索引擎ProteinGoggle 2.0在组蛋白翻译后修饰的自上而下鉴定方面拥有诸多独特的优势。该文报道ProteinGoggle 2.0对HeLa核心组蛋白H4的数据库搜索及蛋白质变体的鉴定结果。基于从UniProt网站下载的人类核心组蛋白H4的纯文本文件和“鸟枪法”注释,ProteinGoggle 2.0首先创建包含所有可能蛋白质变体的理论数据库;从纯文本文件中提取的信息主要是氨基酸序列、可能的翻译后修饰（单甲基化、二甲基化、三甲基化、乙酰化和磷酸化）及氨基酸变异（A77→P）。在控制质谱水平假阳性率低于1%的前提下,共鉴定到426个蛋白质变体,这是目前为止H4蛋白质变体的最全报道。这些ProteinGoggle 2.0鉴定到的H4蛋白质变体也与之前报道的ProSightPC 2.0的鉴定结果进行了肩并肩比较。总而言之,ProteinGoggle 2.0可以对具有复杂组合修饰及氨基酸变异的蛋白质组进行数据库搜索和蛋白质变体鉴定。     

Crystal and Molecular Structure of 4-Hydroxy-3-Methoxy-4-N-Methylstilbazonium Iodide C15H16NO2+·I-

The crystal structure of the title compound C15H16NO2+ · I-(Mr=369. 19) has been determined by single crystal X-ray diffraction analysis. The crystal belongs to tbe monoclinic system with space group P21/c, a=8. 957(1), b=21. 8117(2), c=7. 8760(10)A , β=103.94(1)°, V=1493.8(3)A3, Z=4, Dc=1. 642g cm3,μ=2. 141mm-1, F(000)=728, final R=0. 0264, and Rw=0. 0644(I＞2σ(I)) for 2938 independent reflections. The results show that in the crystal structure of the title compound the planar cations have two configurations, and these cations are anti-parallelly packed through the strong π…π interaction.     

On the viability of small endohedral hydrocarbon cage complexes: X@C4H4, X@C8H8, X@C8H14, X@C10H16, X@C12H12, AND X@C16H16

Small hydrocarbon complexes (X@cage) incorporating cage-centered endohedral atoms and ions (X = H(+), H, He, Ne, Ar, Li(0,+), Be(0,+,2+), Na(0,+), Mg(0,+,2+)) have been studied at the B3LYP/6-31G(d) hybrid HF/DFT level of theory. No tetrahedrane (C(4)H(4), T(d)()) endohedral complexes are minima, not even with the very small hydrogen atom or beryllium dication. Cubane (C(8)H(8), O(h)()) and bicyclo[2.2.2]octane (C(8)H(14), D(3)(h)()) minima are limited to encapsulating species smaller than Ne and Na(+). Despite its intermediate size, adamantane (C(10)H(16), T(d)()) can enclose a wide variety of endohedral atoms and ions including H, He, Ne, Li(0,+), Be(0,+,2+), Na(0,+), and Mg(2+). In contrast, the truncated tetrahedrane (C(12)H(12), T(d)()) encapsulates fewer species, while the D(4)(d)() symmetric C(16)H(16) hydrocarbon cage (see Table of Contents graphic) encapsulates all but the larger Be, Mg, and Mg(+) species. The host cages have more compact geometries when metal atoms, rather than cations, are inside. This is due to electron donation from the endohedral metals into C-C bonding and C-H antibonding cage molecular orbitals. The relative stabilities of endohedral minima are evaluated by comparing their energies (E(endo)) to the sum of their isolated components (E(inc) = E(endo) - E(cage) - E(x)) and to their exohedral isomer energies (E(isom) = E(endo) - E(exo)). Although exohedral binding is preferred to endohedral encapsulation without exception (i.e., E(isom) is always exothermic), Be(2+)@C(10)H(16) (T(d)(); -235.5 kcal/mol), Li(+)@C(12)H(12) (T(d)(); 50.2 kcal/mol), Be(2+)@C(12)H(12) (T(d)(); -181.2 kcal/mol), Mg(2+)@C(12)H(12) (T(d)(); -45.0 kcal/mol), Li(+)@C(16)H(16) (D(4)(d)(); 13.3 kcal/mol), Be(+)@C(16)H(16) (C(4)(v)(); 31.8 kcal/mol), Be(2+)@C(16)H(16) (D(4)(d)(); -239.2 kcal/mol), and Mg(2+)@C(16)H(16) (D(4)(d)(); -37.7 kcal/mol) are relatively stable as compared to experimentally known He@C(20)H(20) (I(h)()), which has an E(inc) = 37.9 kcal/mol and E(isom) = -35.4 kcal/mol. Overall, endohedral cage complexes with low parent cage strain energies, large cage internal cavity volumes, and a small, highly charged guest species are the most viable synthetic targets.     

LSD1: more than demethylation of histone lysine residues

Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer.Subject terms: Epigenetics, Histone post-translational modifications     

Synthesis of a fragment of histone H4 with the sequence 14–21

Summary A fragment of histone H4 with the sequence-Gly-Ala-Lys-Arg-His-Arg-Lys-Val- has been synthesized.V. I. Nikitin Institute of Chemistry, Academy of Sciences of the TadzhSSR, Dushanbe. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 48–51, January–February, 1979.