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4,800 | The Inter-Strand Modes of the DNA as a Probe into MW-Radiation | q-bio.BM | We consider the regime in which the bands of the torsional acoustic (TA) and
the hydrogen-bond-stretch (HBS) modes of the DNA interpenetrate each other.
Within the framework of a model that accommodates the structure of the double
helix, we find the three-wave interaction between the TA- and the HBS-modes,
and show tha... | biology |
4,801 | Differential hydrophobicity drives self-assembly in Huntington's disease | q-bio.BM | Identifying the driving forces and the mechanism of association of
huntingtin-exon1, a close marker for the progress of Huntington's disease, is
an important prerequisite towards finding potential drug targets, and
ultimately a cure. We introduce here a modelling framework based on a key
analogy of the physico-chemical... | biology |
4,802 | Hydration Water Dynamics and Instigation of Protein Structural Relaxation | q-bio.BM | The molecular mechanism of the solvent motion that is required to instigate
the protein structural relaxation above a critical hydration level or
transition temperature has yet to be determined. In this work we use
quasi-elastic neutron scattering (QENS) and molecular dynamics simulation to
investigate hydration water ... | biology |
4,803 | Thermal denaturation and folding rates of single domain proteins: size matters | q-bio.BM | We analyze the dependence of thermal denaturation transition and folding
rates of globular proteins on the number of amino acid residues, N. Using
lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding
transition temperature and DeltaT is the folding transition width. This finding
is consistent with... | biology |
4,804 | Asymmetry in the shapes of folded and denatured states of proteins | q-bio.BM | The asymmetry in the shapes of folded and unfolded states are probed using
two parameters, one being a measure of the sphericity and the other that
describes the shape. For the folded states, whose interiors are densely packed,
the radii of gyration (Rg) and these two parameters are calculated using the
coordinates of ... | biology |
4,805 | Protein secondary structure prediction by combining hidden Markov models and sliding window scores | q-bio.BM | Instead of conformation states of single residues, refined conformation
states of quintuplets are proposed to reflect conformation correlation. Simple
hidden Markov models combining with sliding window scores are used for
predicting secondary structure of a protein from its amino acid sequence. Since
the length of prot... | biology |
4,806 | Protein secondary structure: Entropy, correlations and prediction | q-bio.BM | Is protein secondary structure primarily determined by local interactions
between residues closely spaced along the amino acid backbone, or by non-local
tertiary interactions? To answer this question we have measured the entropy
densities of primary structure and secondary structure sequences, and the local
inter-seque... | biology |
4,807 | Complex folding pathways in a simple beta-hairpin | q-bio.BM | The determination of the folding mechanisms of proteins is critical to
understand the topological change that can propagate Alzheimer and
Creutzfeld-Jakobs diseases, among others. The computational community has paid
considerable attention to this problem; however, the associated time scale,
typically on the order of m... | biology |
4,808 | Analytic models for mechanotransduction: gating a mechanosensitive channel | q-bio.BM | Analytic estimates for the forces and free energy generated by bilayer
deformation reveal a compelling and intuitive model for MscL channel gating
analogous to the nucleation of a second phase. We argue that the competition
between hydrophobic mismatch and tension results in a surprisingly rich story
which can provide ... | biology |
4,809 | Are residues in a protein folding nucleus evolutionarily conserved? | q-bio.BM | It is important to understand how protein folding and evolution influences
each other. Several studies based on entropy calculation correlating
experimental measurement of residue participation in folding nucleus and
sequence conservation have reached different conclusions. Here we report
analysis of conservation of fo... | biology |
4,810 | Coarse-Grained Model of Entropic Allostery | q-bio.BM | Many signalling functions in molecular biology require proteins bind to
substrates such as DNA in response to environmental signals such as the
simultaneous binding to a small molecule. Examples are repressor proteins which
may transmit information via a conformational change in response to the ligand
binding. An alter... | biology |
4,811 | Localization of DNA damage by current exchanging repair enzymes: effects of cooperativity on detection time | q-bio.BM | How DNA repair enzymes find the relatively rare sites of damage is not known
in great detail. Recent experiments and molecular data suggest that the
individual repair enzymes do not work independently of each other, but rather
interact with each other through currents exchanged along DNA. A damaged site
in DNA hinders ... | biology |
4,812 | DNA Renaturation at the Water-Phenol Interface | q-bio.BM | We study DNA adsorption and renaturation in a water-phenol two-phase system,
with or without shaking. In very dilute solutions, single-stranded DNA is
adsorbed at the interface in a salt-dependent manner. At high salt
concentrations the adsorption is irreversible. The adsorption of the
single-stranded DNA is specific t... | biology |
4,813 | Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins | q-bio.BM | Hydrophobicity is thought to be one of the primary forces driving the folding
of proteins. On average, hydrophobic residues occur preferentially in the core,
whereas polar residues tends to occur at the surface of a folded protein. By
analyzing the known protein structures, we quantify the degree to which the
hydrophob... | biology |
4,814 | Modeling DNA Conformational Transformations on the Mesoscopic Scales | q-bio.BM | The approach for the description of the DNA conformational transformations on
the mesoscopic scales in the frame of the double helix is presented. Due to
consideration of the joint motions of DNA structural elements along the
conformational pathways the models for different transformations may be
constructed in the uni... | biology |
4,815 | Ionic effect on combing of single DNA molecules and observation of their force-induced melting by fluorescence microscopy | q-bio.BM | Molecular combing is a powerful and simple method for aligning DNA molecules
onto a surface. Using this technique combined with fluorescence microscopy, we
observed that the length of lambda-DNA molecules was extended to about 1.6
times their contour length (unextended length, 16.2 micrometers) by the combing
method on... | biology |
4,816 | Brownian Dynamics Simulation of Nucleosome Formation and Disruption under Stretching | q-bio.BM | Using a Brownian dynamics simulation, we numerically studied the interaction
of DNA with histone and proposed an octamer-rotation model to describe the
process of nucleosome formation. Nucleosome disruption under stretching was
also simulated. The theoretical curves of extension versus time as well as of
force versus e... | biology |
4,817 | A model for processivity of molecular motors | q-bio.BM | We propose a two-dimensional model for a complete description of the dynamics
of molecular motors, including both the processive movement along track
filaments and the dissociation from the filaments. The theoretical results on
the distributions of the run length and dwell time at a given ATP
concentration, the depende... | biology |
4,818 | Mechanism of unidirectional movement of kinesin motors | q-bio.BM | Kinesin motors have been studied extensively both experimentally and
theoretically. However, the microscopic mechanism of the processive movement of
kinesin is still an open question. In this paper, we propose a hand-over-hand
model for the processivity of kinesin, which is based on chemical, mechanical,
and electrical... | biology |
4,819 | Model for processive movement of myosin V and myosin VI | q-bio.BM | Myosin V and myosin VI are two classes of two-headed molecular motors of the
myosin superfamily that move processively along helical actin filaments in
opposite directions. Here we present a hand-over-hand model for their
processive movements. In the model, the moving direction of a dimeric molecular
motor is automatic... | biology |
4,820 | Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor Properties | q-bio.BM | We describe a faster and more accurate algorithm for computing the
statistical mechanics of DNA denaturation according to the Poland-Scheraga
type. Nearest neighbor thermodynamics is included in a complete and general
way. The algorithm represents an optimization with respect to algorithmic
complexity of the partition ... | biology |
4,821 | Temperature Dependent Conformational Transitions and Hydrogen Bond Dynamics of the Elastin-Like Octapeptide GVG(VPGVG): a Molecular Dynamics Study | q-bio.BM | A joint experimental / theoretical investigation of the elastin-like
octapeptide GVG(VPGVG) was carried out. In this paper a comprehensive molecular
dynamics study of the temperature dependent folding and unfolding of the
octapeptide is presented. The current study, as well as its experimental
counterpart find that thi... | biology |
4,822 | Helix-coil Transition in Closed Circular DNA | q-bio.BM | A simplified model for the closed circular DNA (ccDNA) is proposed to
describe some specific features of the helix-coil transition in such molecule.
The Hamiltonian of ccDNA is related to the one introduced earlier for the
linear DNA. The basic assumption is that the reduced energy of the hydrogen
bond is not constant ... | biology |
4,823 | Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness | q-bio.BM | We develop a simple but rigorous model of protein-protein association
kinetics based on diffusional association on free energy landscapes obtained by
sampling configurations within and surrounding the native complex binding
funnels. Guided by results obtained on exactly solvable model problems, we
transform the problem... | biology |
4,824 | Stability and the Evolvability of Function in a Model Protein | q-bio.BM | Functional proteins must fold with some minimal stability to a structure that
can perform a biochemical task. Here we use a simple model to investigate the
relationship between the stability requirement and the capacity of a protein to
evolve the function of binding to a ligand. Although our model contains no
built-in ... | biology |
4,825 | Dynamics of heterodimeric kinesins and cooperation of kinesins | q-bio.BM | Using the model for the processive movement of a dimeric kinesin we proposed
before, we study the dynamics of a number of mutant homodimeric and
heterodimeric kinesins that were constructed by Kaseda et al. (Kaseda, K.,
Higuchi, H. and Hirose, K. PNAS 99, 16058 (2002)). The theoretical results of
ATPase rate per head, ... | biology |
4,826 | Can contact potentials reliably predict stability of proteins? | q-bio.BM | The simplest approximation of interaction potential between amino-acids in
proteins is the contact potential, which defines the effective free energy of a
protein conformation by a set of amino acid contacts formed in this
conformation. Finding a contact potential capable of predicting free energies
of protein states a... | biology |
4,827 | Vibrational energy relaxation (VER) of a CD stretching mode in cytochrome c | q-bio.BM | We first review how to determine the rate of vibrational energy relaxation
(VER) using perturbation theory. We then apply those theoretical results to the
problem of VER of a CD stretching mode in the protein cytochrome c. We model
cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic
coupling... | biology |
4,828 | Searching low-energy conformations of two elastin sequences | q-bio.BM | The three-dimensional structures of two common repeat motifs
Val$^1$-Pro$^2$-Gly$^3$-Val$^4$-Gly$^5$ and
Val$^1$-Gly$^2$-Val$^3$-Pro$^4$-Gly$^5$-Val$^6$-Gly$^7$-Val$^8$-Pro$^9$ of
tropoelastin are investigated by using the multicanonical simulation procedure.
By minimizing the energy structures along the trajectory the... | biology |
4,829 | Lever-arm and Washboard-potential theories jointly account for Myosin II dynamics | q-bio.BM | We address the controversial hot question concerning the validity of the
loose-coupling versus the lever-arm models in the actomyosin dynamics by
re-interpreting and extending the washboard potential model proposed by some of
us in a previous paper. In the new theory, a loose-coupling mechanism co-exists
with the deter... | biology |
4,830 | Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models | q-bio.BM | In simple models side chains are often represented implicitly (e.g., by
spin-states) or simplified as one atom. We study side chain effects using
square lattice and tetrahedral lattice models, with explicitly side chains of
two atoms. We distinguish effects due to chirality and effects due to side
chain flexibilities, ... | biology |
4,831 | Reconstruction of protein structures from a vectorial representation | q-bio.BM | We show that the contact map of the native structure of globular proteins can
be reconstructed starting from the sole knowledge of the contact map's
principal eigenvector, and present an exact algorithm for this purpose. Our
algorithm yields a unique contact map for all 221 globular structures of
PDBselect25 of length ... | biology |
4,832 | Proteins associated with diseases show enhanced sequence correlation between charged residues | q-bio.BM | Function of proteins or a network of interacting proteins often involves
communication between residues that are well separated in sequence. The classic
example is the participation of distant residues in allosteric regulation.
Bioinformatic and structural analysis methods have been introduced to infer
residues that ar... | biology |
4,833 | Topological thermal instability and length of proteins | q-bio.BM | We present an analysis of the effects of global topology on the structural
stability of folded proteins in thermal equilibrium with a heat bath. For a
large class of single domain proteins, we computed the harmonic spectrum within
the Gaussian Network Model (GNM) and determined the spectral dimension, a
parameter descr... | biology |
4,834 | Geometry and symmetry presculpt the free-energy landscape of proteins | q-bio.BM | We present a simple physical model which demonstrates that the native state
folds of proteins can emerge on the basis of considerations of geometry and
symmetry. We show that the inherent anisotropy of a chain molecule, the
geometrical and energetic constraints placed by the hydrogen bonds and sterics,
and hydrophobici... | biology |
4,835 | The principal eigenvector of contact matrices and hydrophobicity profiles in proteins | q-bio.BM | With the aim to study the relationship between protein sequences and their
native structures, we adopt vectorial representations for both sequence and
structure. The structural representation is based on the Principal Eigenvector
of the fold's contact matrix (PE). As recently shown, the latter encodes
sufficient inform... | biology |
4,836 | Untangling influences of hydrophobicity on protein sequences and structures | q-bio.BM | We fit the Fourier transforms of solvent accessibility and hydrophobicity
profiles of a representative set of proteins to a joint multi-variable
Gaussian. This allows us to separate the intrinsic tendencies of sequence and
structure profiles from the interactions that correlate them; for example, the
$\alpha$-helix per... | biology |
4,837 | Membrane-protein interactions in mechanosensitive channels | q-bio.BM | In this paper, we examine the mechanical role of the lipid bilayer in ion
channel conformation and function with specific reference to the case of the
mechanosensitive channel of large conductance (MscL). In a recent paper
(Wiggins and Phillips, 2004), we argued that mechanotransduction very naturally
arises from lipid... | biology |
4,838 | Forces During Bacteriophage DNA Packaging and Ejection | q-bio.BM | The conjunction of insights from structural biology, solution biochemistry,
genetics and single molecule biophysics has provided a renewed impetus for the
construction of quantitative models of biological processes. One area that has
been a beneficiary of these experimental techniques is the study of viruses. In
this p... | biology |
4,839 | Thermodynamics of beta-amyloid fibril formation | q-bio.BM | Amyloid fibers are aggregates of proteins. They are built out of a peptide
called $\beta$--amyloid (A$\beta$) containing between 41 and 43 residues,
produced by the action of an enzyme which cleaves a much larger protein known
as the Amyloid Precursor Protein (APP). X-ray diffraction experiments have
shown that these f... | biology |
4,840 | Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study | q-bio.BM | The possibility of deriving the contact potentials between amino acids from
their frequencies of occurence in proteins is discussed in evolutionary terms.
This approach allows the use of traditional thermodynamics to describe such
frequencies and, consequently, to develop a strategy to include in the
calculations corre... | biology |
4,841 | Simple models of protein folding and of non--conventional drug design | q-bio.BM | While all the information required for the folding of a protein is contained
in its amino acid sequence, one has not yet learned how to extract this
information to predict the three--dimensional, biologically active, native
conformation of a protein whose sequence is known. Using insight obtained from
simple model simu... | biology |
4,842 | Amino acid substitution matrices for protein conformation identification | q-bio.BM | Methods for alignment of protein sequences typically measure similarity by
using substitution matrix with scores for all possible exchanges of one amino
acid with another. Although widely used, the matrices derived from homologous
sequence segments, such as Dayhoff's PAM matrices and Henikoff's BLOSUM
matrices, are not... | biology |
4,843 | A Constructive Approach to Gene Expression Dynamics | q-bio.BM | The advent of new experimental genomic technologies and the massive increase
of DNA sequence information is helping researchers better understand how our
genes work. Recently, experiments on mRNA abundance (gene expression) have
revealed that gene expression shows a stationary organization described by a
power-law dist... | biology |
4,844 | The effects of non-native interactions on protein folding rates: Theory and simulation | q-bio.BM | Proteins are minimally frustrated polymers. However, for realistic protein
models non-native interactions must be taken into account. In this paper we
analyze the effect of non-native interactions on the folding rate and on the
folding free energy barrier. We present an analytic theory to account for the
modification o... | biology |
4,845 | Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry | q-bio.BM | An effective potential function is critical for protein structure prediction
and folding simulation. For simplified models of proteins where coordinates of
only $C_\alpha$ atoms need to be specified, an accurate potential function is
important. Such a simplified model is essential for efficient search of
conformational... | biology |
4,846 | Order independent structural alignment of circularly permuted proteins | q-bio.BM | Circular permutation connects the N and C termini of a protein and
concurrently cleaves elsewhere in the chain, providing an important mechanism
for generating novel protein fold and functions. However, their in genomes is
unknown because current detection methods can miss many occurances, mistaking
random repeats as c... | biology |
4,847 | Developing optimal nonlinear scoring function for protein design | q-bio.BM | Motivation. Protein design aims to identify sequences compatible with a given
protein fold but incompatible to any alternative folds. To select the correct
sequences and to guide the search process, a design scoring function is
critically important. Such a scoring function should be able to characterize
the global fitn... | biology |
4,848 | Design of a folding inhibitor of the HIV-1 Protease | q-bio.BM | Being HIV-1-PR an essential enzyme in the viral life cycle, its inhibition
can control AIDS. Because the folding of single domain proteins, like HIV-1-PR
is controlled by local elementary structures (LES, folding units stabilized by
strongly interacting, highly conserved amino acids) which have evolved over
myriads of ... | biology |
4,849 | Probing vibrational energy relaxation in proteins using normal modes | q-bio.BM | Vibrational energy relaxation (VER) of a selected mode in cytochrome c
(hemeprotein) in vacuum is studied using two theoretical approaches: One is the
equilibrium simulation approach with quantum correction factors, and the other
is the reduced model approach which describes the protein as an ensemble of
normal modes c... | biology |
4,850 | Oligomerization of amyloid Abeta peptides using hydrogen bonds and hydrophobicity forces | q-bio.BM | The 16-22 amino acid fragment of the beta-amyloid peptide associated with the
Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we
study the aggregation mechanism of Abeta(16-22) peptides by unbiased
thermodynamic simulations at the atomic level for systems of one, three and six
Abeta(16-22) pepti... | biology |
4,851 | Latent periodicity of serine-threonine and tyrosine protein kinases and another protein families | q-bio.BM | We identified latent periodicity in catalytic domains of approximately 85% of
serine/threonine and tyrosine protein kinases. Similar results were obtained
for other 22 protein domains. We also designed the method of noise
decomposition, which is aimed to distinguish between different periodicity
types of the same perio... | biology |
4,852 | Enzyme as a thermal resonance pump | q-bio.BM | We found latent periodicity of 150 protein families now. We suppose that
latent periodicity can determine a spectrum of resonance oscillations in
proteins. | biology |
4,853 | Hidden symmetries in primary sequences of small alpha proteins | q-bio.BM | Proteins have regular tertiary structures but irregular amino acid sequences.
This made it very difficult to decode the structural information in the protein
sequences. Here we demonstrate that many small alpha protein domains have
hidden sequence symmetries characteristic of their pseudo-symmetric tertiary
structures.... | biology |
4,854 | FSSP to SCOP and CATH (F2CS) Prediction Server | q-bio.BM | Summary: The F2CS server provides access to the software, F2CS2.00, that
implements an automated prediction method of SCOP and CATH classifications of
proteins, based on their FSSP Z-scores (Getz et al., 2002), Availability: Free,
at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/. Contact:
eytan.domany@weizma... | biology |
4,855 | A model for the accidental catalysis of protein unfolding in vivo | q-bio.BM | Activated processes such as protein unfolding are highly sensitive to
heterogeneity in the environment. We study a highly simplified model of a
protein in a random heterogeneous environment, a model of the in vivo
environment. It is found that if the heterogeneity is sufficiently large the
total rate of the process is ... | biology |
4,856 | Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins | q-bio.BM | Water molecules and molecular chaperones efficiently help the protein folding
process. Here we describe their action in the context of the energy and
topological networks of proteins. In energy terms water and chaperones were
suggested to decrease the activation energy between various local energy minima
smoothing the ... | biology |
4,857 | Molecular Dynamics Simulations of a Nucleosome and Free DNA | q-bio.BM | Nucleosomes organize the folding of DNA into chromatin and significantly
influence transcription, replication, regulation and repair. All atom molecular
dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in
solution have been conducted. DNA helical parameters are extracted from each
trajectory to... | biology |
4,858 | Specific and non specific hybridization of oligonucleotide probes on microarrays | q-bio.BM | Gene expression analysis by means of microarrays is based on the sequence
specific binding of mRNA to DNA oligonucleotide probes and its measurement
using fluorescent labels. The binding of RNA fragments involving other
sequences than the intended target is problematic because it adds a "chemical
background" to the sig... | biology |
4,859 | Folding is Not Required for Bilayer Insertion: Replica Exchange Simulations of an a-Helical Peptide with an Explicit Lipid Bilayer | q-bio.BM | We implement the replica exchange molecular dynamics algorithm to study the
interactions of a model peptide (WALP-16) with an explicitly represented DPPC
membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16
into the DPPC bilayer and its folding into an a-helix with a trans-bilayer
orientation. We... | biology |
4,860 | Adsorption models of hybridization and post-hybridisation behaviour on oligonucleotide microarrays | q-bio.BM | Analysis of data from an Affymetrix Latin Square spike-in experiment
indicates that measured fluorescence intensities of features on an
oligonucleotide microarray are related to spike-in RNA target concentrations
via a hyperbolic response function, generally identified as a Langmuir
adsorption isotherm. Furthermore the... | biology |
4,861 | Model for processive movement of dynein | q-bio.BM | A model for the processive movement of dynein is presented based on
experimental observations available. In the model, the change from strong
microtubule-binding to weak binding of dynein is determined naturally by the
variation of the relative orientation between the two interacting surfaces of
the stalk tip and the m... | biology |
4,862 | A Phenomenological model of Myosin II dynamics in the presence of external loads | q-bio.BM | We address the controversial hot question concerning the validity of the
loose coupling versus the lever-arm theories in the actomyosin dynamics by
re-interpreting and extending the phenomenological washboard potential model
proposed by some of us in a previous paper. In this new model a Brownian motion
harnessing ther... | biology |
4,863 | Native geometry and the dynamics of protein folding | q-bio.BM | In this paper we investigate the role of native geometry on the kinetics of
protein folding based on simple lattice models and Monte Carlo simulations.
Results obtained within the scope of the Miyazawa-Jernigan indicate the
existence of two dynamical folding regimes depending on the protein chain
length. For chains lar... | biology |
4,864 | The Go model revisited: Native structure and the geometric coupling between local and long-range contacts | q-bio.BM | Monte Carlo simulations show that long-range interactions play a major role
in determining the folding rates of 48-mer three-dimensional lattice polymers
modelled by the Go potential. For three target structures with different native
geometries we found a sharp increase in the folding time when the relative
contributio... | biology |
4,865 | Folding thermodynamics of peptides | q-bio.BM | A simplified interaction potential for protein folding studies at the atomic
level is discussed and tested on a set of peptides with about 20 residues each.
The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,
GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely
sequence-based, i... | biology |
4,866 | Surfaces and orientations: much to fret about? | q-bio.BM | Single molecule FRET (fluorescence resonance energy transfer) is a powerful
technique for detecting real-time conformational changes and molecular
interactions during biological reactions. In this review, we examine different
techniques of extending observation times via immobilization and illustrate how
useful biologi... | biology |
4,867 | Correlations in Systems of Complex Directed Macromolecules | q-bio.BM | An ensemble of directed macromolecules on a lattice is considered, where the
constituting molecules are chosen as a random sequence of N different types.
The same type of molecules experiences a hard-core (exclusion) interaction. We
study the robustness of the macromolecules with respect to breaking and
substituting in... | biology |
4,868 | Ion-Phosphate Mode in the DNA Low-Frequency Spectra | q-bio.BM | The vibrational dynamics of a DNA molecule with counterions neutralizing the
charged phosphate groups have been studied. With the help of elaborated model
the conformational vibrations of the DNA double helix with alkaline metal ions
have been described both qualitatively and quantitatively. For the complexes of
DNA wi... | biology |
4,869 | Conformational transformations of DNA macromolecule in heteronomous conformation | q-bio.BM | To understand the mechanism of TATA-box conformational transformations we
model structure mobility and find the types of conformational excitations of
DNA macromolecule in heteronomous conformation. We have constructed the
two-component model for describing DNA conformational transformation with
simultaneous transition... | biology |
4,870 | Global optimization of proteins using a dynamical lattice model: Ground states and energy landscapes | q-bio.BM | A simple approach is proposed to investigate the protein structure. Using a
low complexity model, a simple pairwise interaction and the concept of global
optimization, we are able to calculate ground states of proteins, which are in
agreement with experimental data. All possible model structures of small
proteins are a... | biology |
4,871 | DNA condensation and redissolution: Interaction between overcharged DNA molecules | q-bio.BM | The effective DNA-DNA interaction force is calculated by computer simulations
with explicit tetravalent counterions and monovalent salt. For overcharged DNA
molecules, the interaction force shows a double-minimum structure. The
positions and depths of these minima are regulated by the counterion density in
the bulk. Us... | biology |
4,872 | A protein structural alphabet and its substitution matrix CLESUM | q-bio.BM | By using a mixture model for the density distribution of the three pseudobond
angles formed by $C_\alpha$ atoms of four consecutive residues, the local
structural states are discretized as 17 conformational letters of a protein
structural alphabet. This coarse-graining procedure converts a 3D structure to
a 1D code seq... | biology |
4,873 | Vibrational energy relaxation in proteins | q-bio.BM | An overview of theories related to vibrational energy relaxation (VER) in
proteins is presented. VER of a selected mode in cytochrome c is studied using
two theoretical approaches. One is the equilibrium simulation approach with
quantum correction factors, and the other is the reduced model approach which
describes the... | biology |
4,874 | Recoverable One-dimensional Encoding of Three-dimensional Protein Structures | q-bio.BM | Protein one-dimensional (1D) structures such as secondary structure and
contact number provide intuitive pictures to understand how the native
three-dimensional (3D) structure of a protein is encoded in the amino acid
sequence. However, it has not been clear whether a given set of 1D structures
contains sufficient info... | biology |
4,875 | Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays | q-bio.BM | The lack of specificity in microarray experiments due to non-specific
hybridization raises a serious problem for the analysis of microarray data
because the residual chemical background intensity is not related to the
expression degree of the gene of interest. We analyzed the concentration
dependence of the signal inte... | biology |
4,876 | Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence | q-bio.BM | Residue-wise contact order (RWCO) is a new kind of one-dimensional protein
structures which represents the extent of long-range contacts. We have recently
shown that a set of three types of one-dimensional structures (secondary
structure, contact number, and RWCO) contains sufficient information for
reconstructing the ... | biology |
4,877 | Heisenberg uncertainty principle for thermal response of the microtubules excited by ultra-short laser pulses | q-bio.BM | In this paper the heat signaling in microtubules (MT) is investigated. It is
argued that for the description of the heat signaling phenomena in MT, the
hyperbolic heat transport (HHT) equation must be used. It is shown that HHT is
the Klein-Gordon (K-G) equation. The general solution for the K-G equation for
MT is obta... | biology |
4,878 | A stochastic approach to multi-gene expression dynamics | q-bio.BM | In the last years, tens of thousands gene expression profiles for cells of
several organisms have been monitored. Gene expression is a complex
transcriptional process where mRNA molecules are translated into proteins,
which control most of the cell functions. In this process, the correlation
among genes is crucial to d... | biology |
4,879 | Early events in insulin fibrillization studied by time-lapse atomic force microscopy | q-bio.BM | The importance of understanding the mechanism of protein aggregation into
insoluble amyloid fibrils relies not only on its medical consequences, but also
on its more basic properties of self--organization. The discovery that a large
number of uncorrelated proteins can form, under proper conditions, structurally
similar... | biology |
4,880 | Helices in Biomolecules | q-bio.BM | Identical objects, regularly assembled, form a helix, which is the principal
motif of nucleic acids, proteins, and viral capsids. | biology |
4,881 | Symmetry and Dynamics in living organisms: The self-similarity principle governs gene expression dynamics | q-bio.BM | The ambitious and ultimate research purpose in Systems Biology is the
understanding and modelling of the cell's system. Although a vast number of
models have been developed in order to extract biological knowledge from
complex systems composed of basic elements as proteins, genes and chemical
compounds, a need remains ... | biology |
4,882 | Universal collective fluctuations in gene expression dynamics from yeast to human | q-bio.BM | In this work, the dynamics of fluctuations in gene expression time series is
investigated. By using collected data of gene expression from yeast and human
organisms, we found that the fluctuations of gene expression level and its
average value over time are strongly correlated and obey a scaling law. As this
feature is... | biology |
4,883 | Controlled DNA compaction within chromatin: the tail-bridging effect | q-bio.BM | We study the mechanism underlying the attraction between nucleosomes, the
fundamental packaging units of DNA inside the chromatin complex. We introduce a
simple model of the nucleosome, the eight-tail colloid, consisting of a charged
sphere with eight oppositely charged, flexible, grafted chains that represent
the term... | biology |
4,884 | Study the effects of metallic ions on the combination of DNA and histones with molecular combing technique | q-bio.BM | The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on
the interaction between DNA and histone are studied using the molecular combing
technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal
cations (Na+, K+, Mg2+, Ca2+, Mn2+) are stretched on hydrophobic surfaces, and
directl... | biology |
4,885 | Functional Dynamics of PDZ Binding Domains: A Normal Mode Analysis | q-bio.BM | PDZ (Post-synaptic density-95/discs large/zonula occludens-1) domains are
relatively small (80 to 120 residues) protein binding modules central in the
organization of receptor clusters and in the association of cellular proteins.
Their main function is to bind C-terminals of selected proteins that are
recognized throug... | biology |
4,886 | Quantifying Influenza Vaccine Efficacy and Antigenic Distance | q-bio.BM | We introduce a new measure of antigenic distance between influenza A vaccine
and circulating strains. The measure correlates well with efficacies of the
H3N2 influenza A component of the annual vaccine between 1971 and 2004, as do
results of a theory of the immune response to influenza following vaccination.
This new m... | biology |
4,887 | Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks | q-bio.BM | Prediction of one-dimensional protein structures such as secondary structures
and contact numbers is useful for the three-dimensional structure prediction
and important for the understanding of sequence-structure relationship. Here we
present a new machine-learning method, critical random networks (CRNs), for
predictin... | biology |
4,888 | Study of a model for the folding of a small protein | q-bio.BM | We describe the results obtained from an improved model for protein folding.
We find that a good agreement with the native structure of a 46 residue long,
five-letter protein segment is obtained by carefully tuning the parameters of
the self-avoiding energy. In particular we find an improved free-energy
profile. We als... | biology |
4,889 | Elastic properties of grafted microtubules | q-bio.BM | We use single-particle tracking to study the elastic properties of single
microtubules grafted to a substrate. Thermal fluctuations of the free
microtubule's end are recorded, in order to measure position distribution
functions from which we calculate the persistence length of microtubules with
contour lengths between ... | biology |
4,890 | Free energy adopted stochastic optimization protein folding | q-bio.BM | Optimal structure of proteins is described by linear stochastic differential
equation with mean decrease of free energy and volatility. Structure
determining strategy is given by a twin of stochastic variables for which
empirical conditions are not postulated. Optimal structure determination will
be deformed to be adop... | biology |
4,891 | Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers | q-bio.BM | One of the main problems of drug design is that of optimizing the
drug--target interaction. In the case in which the target is a viral protein
displaying a high mutation rate, a second problem arises, namely the eventual
development of resistance. We wish to suggest a scheme for the design of
non--conventional drugs wh... | biology |
4,892 | Geometric and physical considerations for realistic protein models | q-bio.BM | Protein structure is generally conceptualized as the global arrangement or of
smaller, local motifs of helices, sheets, and loops. These regular, recurring
secondary structural elements have well-understood and standardized definitions
in terms of amino acid backbone geometry and the manner in which hydrogen
bonding re... | biology |
4,893 | Structure calculation strategies for helical membrane proteins; a comparison study | q-bio.BM | Structure predictions of helical membrane proteins have been designed to take
advantage of the structural autonomy of secondary structure elements, as
postulated by the two-stage model of Engelman and Popot. In this context, we
investigate structure calculation strategies for two membrane proteins with
different functi... | biology |
4,894 | Inferring interactions from combinatorial protein libraries | q-bio.BM | Proteins created by combinatorial methods in vitro are an important source of
information for understanding sequence-structure-function relationships.
Alignments of folded proteins from combinatorial libraries can be analyzed
using methods developed for naturally occurring proteins, but this neglects the
information co... | biology |
4,895 | Design of amino acid sequences to fold into C_alpha-model proteins | q-bio.BM | In order to extend the results obtained with minimal lattice models to more
realistic systems, we study a model where proteins are described as a chain of
20 kinds of structureless amino acids moving in a continuum space and
interacting through a contact potential controlled by a 20x20 quenched random
matrix. The goal ... | biology |
4,896 | Geometrical model for the native-state folds of proteins | q-bio.BM | We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci.
USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which
incorporates, in an approximate manner, several key features such as the
inherent anisotropy of a chain molecule, the geometrical and energetic
constraints placed by the hydroge... | biology |
4,897 | The histone octamer influences the wrapping direction of DNA on it: Brownian dynamics simulation of the nucleosome chirality | q-bio.BM | In eukaryote nucleosome, DNA wraps around a histone octamer in a left-handed
way. We study the process of chirality formation of nucleosome with Brownian
dynamics simulation. We model the histone octamer with a quantitatively
adjustable chirality: left-handed, right-handed or non-chiral, and simulate the
dynamical wrap... | biology |
4,898 | Specificity of Trypsin and Chymotrypsin: Loop Motion Controlled Dynamic Correlation as a Determinant | q-bio.BM | Trypsin and chymotrypsin are both serine proteases with high sequence and
structural similarities, but with different substrate specificity. Previous
experiments have demonstrated the critical role of the two loops outside the
binding pocket in controlling the specificity of the two enzymes. To understand
the mechanism... | biology |
4,899 | Spatial dynamics of homochiralization | q-bio.BM | The emergence and spreading of chirality on the early Earth is considered by
studying a set of reaction-diffusion equations based on a polymerization model.
It is found that effective mixing of the early oceans is necessary to reach the
present homochiral state. The possibility of introducing mass extinctions and
modif... | biology |
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