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Relationship Between Structural Fractal and Possible Dynamic Scaling Properties in Protein Folding  [PDF]
Liang-Jian Zou,X. G. Gong,Zheng-Gang Zhu
Physics , 1996,
Abstract: In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal dimensionality may exist only for short sequences in large protein molecules and small protein molecules with homogeneous structure, the fractal dimensionality are obtained for different structures. We then show that there might exist the dynamic scaling properties in protein folding, the critical exponents in the folding for some small global proteins with homogeneous structure are obtained. The dynamic critical exponents of the global proteins in folding are relevant to the fractal dimensionality of its structure, which implies the close relationship between the dynamic process in protein folding and its structure kinematics.
Meta-Analysis of General Bacterial Subclades in Whole-Genome Phylogenies Using Tree Topology Profiling
Thomas Meinel and Antje Krause
Evolutionary Bioinformatics , 2012, DOI: 10.4137/EBO.S9642
Abstract: In the last two decades, a large number of whole-genome phylogenies have been inferred to reconstruct the Tree of Life (ToL). Underlying data models range from gene or functionality content in species to phylogenetic gene family trees and multiple sequence alignments of concatenated protein sequences. Diversity in data models together with the use of different tree reconstruction techniques, disruptive biological effects and the steadily increasing number of genomes have led to a huge diversity in published phylogenies. Comparison of those and, moreover, identification of the impact of inference properties (underlying data model, inference technique) on particular reconstructions is almost impossible. In this work, we introduce tree topology profiling as a method to compare already published whole-genome phylogenies. This method requires visual determination of the particular topology in a drawn whole-genome phylogeny for a set of particular bacterial clans. For each clan, neighborhoods to other bacteria are collected into a catalogue of generalized alternative topologies. Particular topology alternatives found for an ordered list of bacterial clans reveal a topology profile that represents the analyzed phylogeny. To simulate the inhomogeneity of published gene content phylogenies we generate a set of seven phylogenies using different inference techniques and the SYSTERS-PhyloMatrix data model. After tree topology profiling on in total 54 selected published and newly inferred phylogenies, we separate artefactual from biologically meaningful phylogenies and associate particular inference results (phylogenies) with inference background (inference techniques as well as data models). Topological relationships of particular bacterial species groups are presented. With this work we introduce tree topology profiling into the scientific field of comparative phylogenomics.
Scaling properties of evolutionary paths in a biophysical model of protein adaptation  [PDF]
Michael Manhart,Alexandre V. Morozov
Quantitative Biology , 2014, DOI: 10.1088/1478-3975/12/4/045001
Abstract: The enormous size and complexity of genotypic sequence space frequently requires consideration of coarse-grained sequences in empirical models. We develop scaling relations to quantify the effect of this coarse-graining on properties of fitness landscapes and evolutionary paths. We first consider evolution on a simple Mount Fuji fitness landscape, focusing on how the length and predictability of evolutionary paths scale with the coarse-grained sequence length and alphabet. We obtain simple scaling relations for both the weak- and strong-selection limits, with a non-trivial crossover regime at intermediate selection strengths. We apply these results to evolution on a biophysical fitness landscape that describes how proteins evolve new binding interactions while maintaining their folding stability. We combine the scaling relations with numerical calculations for coarse-grained protein sequences to obtain quantitative properties of the model for realistic binding interfaces and a full amino acid alphabet.
The shape of human gene family phylogenies
James A Cotton, Roderic DM Page
BMC Evolutionary Biology , 2006, DOI: 10.1186/1471-2148-6-66
Abstract: We find that gene duplication has produced gene family trees significantly less balanced than expected from a simple model of the process, and less balanced than species phylogenies: the opposite to what might be expected under the 2R hypothesis.While other explanations are plausible, we suggest that the greater imbalance of gene family trees than species trees is due to the prevalence of tandem duplications over regional duplications during the evolution of the human genome.Most phylogenetic trees represent the evolutionary history of groups of organisms, with the leaves representing species (or higher taxa) and internal nodes representing speciation events. In contrast, molecular phylogenies for gene families (e.g. figure 1a) usually display sequences for different orthologous groups of proteins [1] from one or more species. These trees can thus show a complicated tapestry of orthology and paralogy, and nodes on such trees may represent either gene duplications or speciations (figure 1, [2]): both are splitting events, producing daughter lineages that henceforth have independent evolutionary histories (at least in the absence of gene conversion or introgression [3]). This similarity between gene duplication and speciation allows similar tools to be used to study the two analogous processes, and techniques developed to investigate speciation and extinction may give some insight into the pattern of gene duplication and gene loss [4,5].Tree shape has been used to make inferences about the processes of speciation and extinction that govern the birth and death of organismal lineages [6]. We can similarly investigate the processes of gene duplication and gene loss, or deletion, on phylogenies where all the nodes represent gene duplication events, such as those containing homologous genes from a single genome (figure 1). In particular, gene sequences from a completely sequenced genome allow inferences about the process of deletion to be made without confounding this with
Dynamical family properties and dark halo scaling relations of giant elliptical galaxies  [PDF]
Ortwin Gerhard,Andi Kronawitter,R. P. Saglia,Ralf Bender
Physics , 2000, DOI: 10.1086/319940
Abstract: Based on a uniform dynamical analysis of line-profile shapes for 21 luminous round elliptical galaxies, we have investigated the dynamical family relations of ellipticals: (i) The circular velocity curves (CVCs) of elliptical galaxies are flat to within ~10% for R>~0.2R_e. (ii) Most ellipticals are moderately radially anisotropic; their dynamical structure is surprisingly uniform. (iii) Elliptical galaxies follow a Tully-Fisher (TF) relation, with v_c^max=300 km/s for an L_B^* galaxy. At given v_c^max, they are ~1 mag fainter in B and appear to have slightly lower baryonic mass than spirals even for maximum M/L_B. (iv) The luminosity dependence of M/L_B is confirmed. The tilt of the Fundamental Plane is not caused by dynamical non-homology, nor only by an increasing dark matter fraction with L. It is, however, consistent with stellar population models based on published metallicities and ages. The main driver is therefore probably metallicity, and a secondary population effect is needed to explain the K-band tilt. (v) These results make it likely that elliptical galaxies have nearly maximal M/L_B (minimal halos). (vi) Despite the uniformly flat CVCs, there is a spread in cumulative M/L_B(r). Some galaxies have no indication for dark matter within 2R_e, whereas others have local M/L_Bs of 20-30 at 2R_e. (vii) In models with maximum stellar mass, the dark matter contributes ~10-40% of the mass within R_e. (viii) The corresponding halo core densities and phase-space densities are at least ~25 times larger and the halo core radii ~4 times smaller than in spiral galaxies of the same v_c^max. The increase in M/L sets in at ~10 times larger acceleration than in spirals. This could imply that elliptical galaxy halos collapsed at high redshift or that some of the dark matter in ellipticals might be baryonic. (abridged)
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
Dennis R Livesay, Dang H Huynh, Sargis Dallakyan, Donald J Jacobs
Chemistry Central Journal , 2008, DOI: 10.1186/1752-153x-2-17
Abstract: We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods t
Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group
Timothy R Schmidt, Edgar J Scott, David W Dyer
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-430
Abstract: Phylogenetic analysis of the Bc species-group utilizing 157 single-copy genes of the family Bacillaceae suggests that several taxonomic revisions of the genus Bacillus should be considered. Within the Bc species-group there is little indication that the currently recognized species form related sub-groupings, suggesting that they are members of the same species. The sigma factor gene family encoded by the Bc species-group appears to be the result of a dynamic gene-duplication and gene-loss process that in previous analyses underestimated the true heterogeneity of the sigma factor content in the Bc species-group.Expansion of the sigma factor gene family appears to have preferentially occurred within the extracytoplasmic function (ECF) sigma factor genes, while the primary alternative (PA) sigma factor genes are, in general, highly conserved with those found in B. subtilis. Divergence of the sigma-controlled transcriptional regulons among various members of the Bc species-group likely has a major role in explaining the diversity of phenotypic characteristics seen in members of the Bc species-group.The genus Bacillus consists of a heterogeneous group of Gram-positive heterotrophic aerobic or facultative anaerobic bacilli with the ability to form environmentally resistant, metabolically inert spores [1]. These soil-borne organisms are ubiquitous throughout the world, and occupy surprisingly diverse environments [2,3]. Within this large genus, the B. cereus sensu lato group consists of six species [B. anthracis (Ba), B. cereus (Bc), B. mycoides, B. pseudomycoides, B. thuringiensis (Bt), and B. weihenstephanensis], based on classical microbial taxonomy [4]. However, newer molecular phylogenies and comparative genome sequencing suggests that these organisms should be classified as a single species [5]. On the surface, this conclusion seems difficult to reconcile with the varied biological characteristics of these organisms. Some Bc strains are thermophiles [6], while B. we
Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin  [PDF]
Jesse D. Bloom ,Matthew J. Glassman
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000349
Abstract: One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution.
Characterization of a Gene Family Encoding SEA (Sea-urchin Sperm Protein, Enterokinase and Agrin)-Domain Proteins with Lectin-Like and Heme-Binding Properties from Schistosoma japonicum  [PDF]
Evaristus Chibunna Mbanefo,Mihoko Kikuchi,Nguyen Tien Huy,Mohammed Nasir Shuaibu,Mahamoud Sama Cherif,Chuanxin Yu,Masahiro Wakao,Yasuo Suda,Kenji Hirayama
PLOS Neglected Tropical Diseases , 2014, DOI: 10.1371/journal.pntd.0002644
Abstract: Background We previously identified a novel gene family dispersed in the genome of Schistosoma japonicum by retrotransposon-mediated gene duplication mechanism. Although many transcripts were identified, no homolog was readily identifiable from sequence information. Methodology/Principal Findings Here, we utilized structural homology modeling and biochemical methods to identify remote homologs, and characterized the gene products as SEA (sea-urchin sperm protein, enterokinase and agrin)-domain containing proteins. A common extracellular domain in this family was structurally similar to SEA-domain. SEA-domain is primarily a structural domain, known to assist or regulate binding to glycans. Recombinant proteins from three members of this gene family specifically interacted with glycosaminoglycans with high affinity, with potential implication in ligand acquisition and immune evasion. Similar approach was used to identify a heme-binding site on the SEA-domain. The heme-binding mode showed heme molecule inserted into a hydrophobic pocket, with heme iron putatively coordinated to two histidine axial ligands. Heme-binding properties were confirmed using biochemical assays and UV-visible absorption spectroscopy, which showed high affinity heme-binding (KD = 1.605×10?6 M) and cognate spectroscopic attributes of hexa-coordinated heme iron. The native proteins were oligomers, antigenic, and are localized on adult worm teguments and gastrodermis; major host-parasite interfaces and site for heme detoxification and acquisition. Conclusions The results suggest potential role, at least in the nucleation step of heme crystallization (hemozoin formation), and as receptors for heme uptake. Survival strategies exploited by parasites, including heme homeostasis mechanism in hemoparasites, are paramount for successful parasitism. Thus, assessing prospects for application in disease intervention is warranted.
Scaling properties of the Penna model  [PDF]
E. Brigatti,J. S. Sa' Martins,I. Roditi
Quantitative Biology , 2005, DOI: 10.1140/epjb/e2004-00400-x
Abstract: We investigate the scaling properties of the Penna model, which has become a popular tool for the study of population dynamics and evolutionary problems in recent years. We find that the model generates a normalised age distribution for which a simple scaling rule is proposed, that is able to reproduce qualitative features for all genome sizes.
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