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排序方式: 共有241条查询结果,搜索用时 15 毫秒
1.
Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics‐inspired motion planning procedure called dCC‐RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non‐native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC‐RRT to examine how collective, small‐scale motions of four side‐chains in the active site of cyclophilin A propagate through the protein. dCC‐RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non‐canonical capsid binding site 25 Å away, rationalizing NMR and multi‐temperature crystallography experiments. In all, dCC‐RRT can reveal detailed, all‐atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/ .  相似文献   
2.
魏偏偏 《人类学学报》2020,39(4):616-631
1960年,在云南省丽江市发现了三根古人类股骨,通过地层观察,仅PA108可归为更新世晚期。前人对PA108做了初步报导,为了进一步了解丽江人股骨的演化分类地位和东亚早期现代人股骨形态变异,本文对PA108的内外结构进行了详尽的分析。研究发现,PA108具有明显的早期现代人特征,即明显的股骨粗线、骨干中部后侧骨密质最厚和中部横断面轮廓形状偏椭圆。PA108标本也有一定的特殊性,体现在骨干中近端和中部骨密质厚度分布上,这可能与其股骨嵴发育较弱有关,这一特征也导致了PA108与其他东亚早期现代人之间的形态差异,这些形态变异进一步扩大了目前已知的东亚地区早期现代人变异范围。同时,在采用骨密质厚度分布模式进行分类时,建议关注股骨骨干中部骨密质最厚部位。  相似文献   
3.
Sexual selection may cause dietary requirements for reproduction to diverge across the sexes and promote the evolution of different foraging strategies in males and females. However, our understanding of how the sexes regulate their nutrition and the effects that this has on sex‐specific fitness is limited. We quantified how protein (P) and carbohydrate (C) intakes affect reproductive traits in male (pheromone expression) and female (clutch size and gestation time) cockroaches (Nauphoeta cinerea). We then determined how the sexes regulate their intake of nutrients when restricted to a single diet and when given dietary choice and how this affected expression of these important reproductive traits. Pheromone levels that improve male attractiveness, female clutch size and gestation time all peaked at a high daily intake of P:C in a 1:8 ratio. This is surprising because female insects typically require more P than males to maximize reproduction. The relatively low P requirement of females may reflect the action of cockroach endosymbionts that help recycle stored nitrogen for protein synthesis. When constrained to a single diet, both sexes prioritized regulating their daily intake of P over C, although this prioritization was stronger in females than males. When given the choice between diets, both sexes actively regulated their intake of nutrients at a 1:4.8 P:C ratio. The P:C ratio did not overlap exactly with the intake of nutrients that optimized reproductive trait expression. Despite this, cockroaches of both sexes that were given dietary choice generally improved the mean and reduced the variance in all reproductive traits we measured relative to animals fed a single diet from the diet choice pair. This pattern was not as strong when compared to the single best diet in our geometric array, suggesting that the relationship between nutrient balancing and reproduction is complex in this species.  相似文献   
4.
昂立植物乳杆菌对腹腔感染大鼠肠道微生态的影响   总被引:2,自引:0,他引:2  
目的探讨经肠道补充昂立植物乳杆菌(LP-Onlly)对腹腔感染大鼠肠道微生态的影响.方法大鼠经盲肠结扎穿孔法及颈静脉空肠置管制成腹腔感染模型后,分别给予肠外营养(PN组)和PN 昂立植物乳杆菌(LP-Onlly组)持续5 d,第6天处死,取盲肠内粪便进行肠菌群培养计数及细菌种群DNA指纹图谱分析.结果 LP-Onlly组大鼠肠道内的乳杆菌和双歧杆菌数量较单纯PN组的大鼠为多,而肠道内的潜在致病菌产气荚膜梭菌数量较单纯PN组的大鼠少,DNA指纹图谱也显示LP-Onlly组大鼠优势菌群的基因条带和正常大鼠具有较高的一致性,而PN组则差异有显著性.结论 LP-Onlly能纠正腹腔感染大鼠PN时的肠道菌群紊乱, 调理肠道微生态平衡.  相似文献   
5.
The absolute volume of biological objects is often estimated stereologically from an exhaustive set of systematic sections. The usual volume estimator is the sum of the section contents times the distance between sections. For systematic sectioning with a random start, it has been recently shown that is unbiased when m, the ratio between projected object length and section distance, is an integer number (Cruz-Orive 1985). As this quantity is no integer in the real world, we have explored the properties of in the general and realistic situation m . The unbiasedness of under appropriate sampling conditions is demonstrated for the arbitrary compact set in 3 dimensions by a rigorous proof. Exploration of further properties of for the general triaxial ellipsoid leads to a new class of non-elementary real functions with common formal structure which we denote as np-functions. The relative mean square error (CE 2) of in ellipsoids is an oscillating differentiable np-function, which reduces to the known result CE 2= 1/(5m 4) for integer m. As a biological example the absolute volumes of 10 left cardiac ventricles and their internal cavities were estimated from systematic sections. Monte Carlo simulation of replicated systematic sectioning is shown to be improved by using m instead of m . In agreement with the geometric model of ellipsoids with some added shape irregularities, mean empirical CE was proportional to m –1.36 and m–1.73 in the cardiac ventricle and its cavity. The considerable variance reduction by systematic sectioning is shown to be a geometric realization of the principle of antithetic variates.  相似文献   
6.
Recent null models that place species ranges randomly within a bounded domain have produced controversial results. Many such geometric constraint models predict a peak in species richness in the centre of domains in the absence of underlying environmental gradients or interspecific interactions. We used two-dimensional simulation models to explore different ways that species ranges could interact with the domain boundary. In the rejection model, a randomly generated range that overlaps a domain boundary is removed from the simulation. In the reshaping model, a range that overlaps the domain boundary is reshaped so that the entire range is placed within the domain. The truncation model allows potential ranges to extend across the boundary, but only that portion of the range within the domain is included in the realized range. Both rejection and reshaping models produced a drop in species richness near domain boundaries, though the effect was less pronounced in the reshaping model. Our truncation model did not produce any spatial pattern in species richness. Thus the random placement of species ranges within a bounded domain does not necessarily lead to a mid-domain effect.
  Range truncation is consistent with bioclimate envelope models, which can successfully predict a species range in response to the availability of appropriate climate conditions. We argue that such flexible range sizes are more realistic than the assumption that range size is an unvarying characteristic of a species. Other range characteristics, including size and shape, can change near domain boundaries in the null models, including the truncation model. A broader consideration of range characteristics near domain boundaries could be productive.  相似文献   
7.
Energy calculations have been carried out on high-symmetry cuboctahedral Ni-Al nanoalloy clusters, of varying composition, with the interatomic interactions modelled by the Gupta many-body potential. Relaxations of cuboctahedral fragments cut from the bulk lattice of Ni3Al, with 13-561 atoms, were undertaken, as were relaxations of high symmetry clusters with 55 and 147 atoms. The lowest energy isomers were found to be dominated by three factors: the tendency toward mixing due to the favourable energy of mixing, ΔmixE; the size difference between nickel and aluminium; and the higher cohesive and surface energy of nickel compared to aluminium. The latter two factors favour Al-segregation to the surface. The most stable Ni:Al composition approaches 3:1 for larger clusters.  相似文献   
8.
Alpha-14 giardin (annexin E1), a member of the alpha giardin family of annexins, has been shown to localize to the flagella of the intestinal protozoan parasite Giardia lamblia. Alpha giardins show a common ancestry with the annexins, a family of proteins most of which bind to phospholipids and cellular membranes in a Ca2+-dependent manner and are implicated in numerous membrane-related processes including cytoskeletal rearrangements and membrane organization. It has been proposed that alpha-14 giardin may play a significant role during the cytoskeletal rearrangement during differentiation of Giardia. To gain a better understanding of alpha-14 giardin's mode of action and its biological role, we have determined the three-dimensional structure of alpha-14 giardin and its phospholipid-binding properties. Here, we report the apo crystal structure of alpha-14 giardin determined in two different crystal forms as well as the Ca2+-bound crystal structure of alpha-14 giardin, refined to 1.9, 1.6 and 1.65 Å, respectively. Although the overall fold of alpha-14 giardin is similar to that of alpha-11 giardin, multiwavelength anomalous dispersion phasing was required to solve the alpha-14 giardin structure, indicating significant structural differences between these two members of the alpha giardin family. Unlike most annexin structures, which typically possess N-terminal domains, alpha-14 giardin is composed of only a core domain, followed by a C-terminal extension that may serve as a ligand for binding to cytoskeletal protein partners in Giardia. In the Ca2+-bound structure we detected five bound calcium ions, one of which is a novel, highly coordinated calcium-binding site not previously observed in annexin structures. This novel high-affinity calcium-binding site is composed of seven protein donor groups, a feature rarely observed in crystal structures. In addition, phospholipid-binding assays suggest that alpha-14 giardin exhibits calcium-dependent binding to phospholipids that coordinate cytoskeletal disassembly/assembly during differentiation of the parasite.  相似文献   
9.
The unique set of morphological characteristics of the Liang Bua hominins (Homo floresiensis) has been attributed to explanations as diverse as insular dwarfism and pathological microcephaly. This study examined the relationship between cranial size and shape across a range of hominin and African ape species to test whether or not cranial morphology of LB1 is consistent with the basic pattern of static allometry present in these various taxa. Correlations between size and 3D cranial shape were explored using principal components analysis in shape space and in Procrustes form space. Additionally, patterns of static allometry within both modern humans and Plio-Pleistocene hominins were used to simulate the expected cranial shapes of each group at the size of LB1. These hypothetical specimens were compared to LB1 both visually and statistically. Results of most analyses indicated that LB1 best fits predictions for a small specimen of fossil Homo but not for a small modern human. This was especially true for analyses of neurocranial landmarks. Results from the whole cranium were less clear about the specific affinities of LB1, but, importantly, demonstrated that aspects of facial morphology associated with smaller size converge on modern human morphology. This suggests that facial similarities between LB1 and anatomically modern humans may not be indicative of a close relationship. Landmark data collected from this study were also used to test the degree of cranial asymmetry in LB1. These comparisons indicated that the cranium is fairly asymmetrical, but within the range of asymmetry exhibited by modern humans and all extant African ape species. Compared to other fossil specimens, the degree of asymmetry in LB1 is moderate and readily explained by the taphonomic processes to which all fossils are subject. Taken together, these findings suggest that H. floresiensis was most likely the diminutive descendant of a species of archaic Homo, although the details of this evolutionary history remain obscure.  相似文献   
10.
To elucidate the structural basis of the diversity and universality in protein-protein interactions, an exhaustive all-against-all structural comparison of all known protein interfaces in the Protein Data Bank was performed at atomic resolution. After similar interfaces were clustered, approximately 20,000 structural motifs with at least two members were identified, out of which 3678 motifs consisted of at least 10 interfaces. Except for some trivial interfaces involving single α helices, almost all motifs were found to be confined within single protein families. Furthermore, the interaction partners of each motif were found to be very limited, and, accordingly, the interaction networks of the motifs tend to be small and are much more restricted than the binding sites for small ligand molecules. These findings suggest that, at the level of atomic structures, protein-protein interactions are precisely designed; hence, protein interfaces with multiple interacting partners should involve incompletely overlapping multiple interfaces and/or accommodate structural changes upon binding to their targets.  相似文献   
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