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Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. |
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy between thermal and quantum diffusion: by writing the solution of the Fokker-Pla... |
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 th... |
Superoxide reductase (SOR) catalyzes the reduction of O2*- to H2O2. Its active site consists of a non-heme Fe2+ center in an unusual square-pyramidal [His4 Cys] coordination. |
The strength or weakness of an algorithm is ultimately governed by the confidence of its result. When the domain of the problem is large (e.g. traversal of a high-dimensional space), a perfect solution cannot be obtained, so approximations must be made. |
Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the languages in biology and chemistry. |
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete sampling of a biopolymer's many degrees of freedom. |
Liquid-liquid phase separation of charge/aromatic-enriched intrinsically disordered proteins (IDPs) is critical in the biological function of membraneless organelles. Much of the physics of this recent discovery remains to be elucidated. |
The Goldman-Hodgkin-Katz (GHK) equations have been widely applied to ion channel studies, simulations, and model developments. However, they are constructed under a constant electric field, causing them to have a low degree of approximation in the prediction of ionic fluxes, electric currents, and membrane potentials.... |
The need of new diagnostic methods satisfying, as an early detection, a low invasive procedure and a cost-efficient value, is orienting the technological research toward the use of bio-integrated devices, in particular bio-sensors. The set of know-why necessary to achieve this goal is wide, from biochemistry to electr... |
The phase coherence relaxation times as long as $T_2\sim830-1030\pm20$ ns were measured for the [2Fe-2S] cluster in the intrinsic protein environment. This relaxation corresponds to a relatively long lasting coherence of the low-spin $S=1/2$ state. |
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two different co-solvents of water, urea and dimethyl sulphoxide (DMSO), and study unf... |
The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is restricted, divalent counterions can cause DNA reentrant condensation similar to that ca... |
In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the B... |
Large language models (LLMs) have garnered considerable attention for their proficiency in tackling intricate tasks, particularly leveraging their capacities for zero-shot and in-context learning. However, their utility has been predominantly restricted to general tasks due to an absence of domain-specific knowledge. |
As a necessary process in drug development, finding a drug compound that can selectively bind to a specific protein is highly challenging and costly. Drug-target affinity (DTA), which represents the strength of drug-target interaction (DTI), has played an important role in the DTI prediction task over the past decade.... |
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules distinction is followed by specific balanced atom number and/or nucleon number ... |
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key molecular resources constituting CRISPRa by the orthogonal short RNA that guide... |
The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, dataset, and seed bias impact the technology's utility to medicine and computational chemists. |
The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. |
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their complements, and 6 non-complements) are observed now together with two furt... |
In this paper, we utilized generative models, and reformulate it for problems in molecular dynamics (MD) simulation, by introducing an MD potential energy component to our generative model. By incorporating potential energy as calculated from TorchMD into a conditional generative framework, we attempt to construct a l... |
We develop a quantum scattering model to describe the exciton transport through the Fenna-Matthews-Olson(FMO) complex. It is found that the exciton transport involved the optimal quantum coherence is more efficient than that involved classical behavior alone. |
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology but adaptively assemble into different icosahedral morphologies around... |
We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. |
Mutations create the genetic diversity on which selective pressures can act, yet also create structural instability in proteins. How, then, is it possible for organisms to ameliorate mutation-induced perturbations of protein stability while maintaining biological fitness and gaining a selective advantage? |
Antibiotic resistance is a topical problem for both humans and animals and has been the subject of special monitoring for two decades. Several recent studies, including ours, have shown that this phenomenon is accentuated by the transfer of certain genetic elements and cross resistance acquisition, the latter or both ... |
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. |
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. |
Resonance assignment is a critical first step in the investigation of protein structures using NMR spectroscopy. The development of assignment methods that require less experimental data is possible with prior knowledge of the macromolecular structure. |
A construction method for duplex cage structures with icosahedral sym- metry made out of single-stranded DNA molecules is presented and applied to an icosidodecahedral cage. It is shown via a mixture of analytic and computer techniques that there exist realisations of this graph in terms of two circular DNA molecules.... |
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). |
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. |
Sensitive and reliable methylation assay is important for oncogentic studies and clinical applications. Here, a new methylation assay was developed by the use of adapter-dependent adapter in library preparation. |
The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. |
Aims: Over the past two decades, the rise of multidrug resistance (MDR) in bacteria has posed a significant threat to global health. The urgent need for new treatment alternatives has brought attention to the potential of plants, which harbor a wealth of unexplored phytochemicals with therapeutic properties. |
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. |
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow timescales. A promising approach to enhanced sampling of MSMs is to use so-c... |
ESPSim is an open source JAVA program that enables the comparisons of protein electrostatic potential maps via the computation of an electrostatic similarity measure. This program has been utilized to demonstrate a high degree of electrostatic similarity among the potential maps of lysozyme proteins, suggesting that p... |
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural ensembles. Here we introduce a statistical coupling analysis for repeat proteins -- nat... |
We investigate the transport of proteins inside the proteasome and propose an active transport mechanism based on a spatially asymmetric interaction potential of peptide chains. The transport is driven by fluctuations which are always present in such systems. |
Directed evolution of proteins has been the most effective method for protein engineering. However, a new paradigm is emerging, fusing the library generation and screening approaches of traditional directed evolution with computation through the training of machine learning models on protein sequence fitness data. |
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered by deep learning to address this problem, we introduce a Molecular Dynamics Lar... |
Recently, machine learning (ML) has gained popularity in the early stages of drug discovery. This trend is unsurprising given the increasing volume of relevant experimental data and the continuous improvement of ML algorithms. |
In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. LB126 were investigated. |
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. |
Peptide design plays a pivotal role in therapeutics, allowing brand new possibility to leverage target binding sites that are previously undruggable. Most existing methods are either inefficient or only concerned with the target-agnostic design of 1D sequences. |
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. |
Designing synthetically accessible molecules and recommending analogs to unsynthesizable molecules are important problems for accelerating molecular discovery. We reconceptualize both problems using ideas from program synthesis. |
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including disordered proteins, multi-domain proteins, proteins in crowded environments, and dis... |
Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++, and Cl-. |
Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. |
To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transcription of TPP riboswitch expression platforms. |
With the aid of quantum mechanical calculations we investigate the electronic structure of the full length (FL) potassium channel protein, FL-KcsA, in its closed conformation, and the electronic structure of the ClC chloride channel. The results indicate that both ion channels are strongly polarized towards the extrac... |
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. |
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. |
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. |
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic. This review sets out to explore the computational prediction of RNA secondary ... |
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past decade with different approaches, such as structural characterization, in vitro... |
The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling through the intermolecular potential barrier is essential. |
Peroxisome proliferator-activated receptors gamma (PPAR{\gamma}) are ligand-activated controllers of various metabolic actions and insulin sensitivity. PPAR{\gamma} is thus considered as an important target to treat type 2 diabetes. |
The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. |
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that |
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. |
Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations requires sophisticated, expensive, and time-consuming wet-lab experiments that can be ... |
Graph neural networks have become a powerful framework for learning complex structure-property relationships and fast screening of chemical compounds. Recently proposed methods have demonstrated that using 3D geometry information of the molecule along with the bonding structure can lead to more accurate prediction on ... |
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). |
The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains challenging due to their highly dynamic nature and the scarcity of experimentally solved binding data. To address this problem, we built an unprecedentedly larg... |
Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have compromised existing vaccines and posed a grand challenge to coronavirus disease 2019 (COVID-19) prevention, control, and global economic recovery. For COVID-19 patients, one of the most effective COVID-19 medications is monoclonal ant... |
Ion channels are proteins with holes down their middle that control the flow of ions and electric current across otherwise impermeable biological membranes. The flow of sodium, potassium, calcium (divalent), and chloride ions have been central issues in biology for more than a century. |
Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a membrane-mimicking (DMSO) solution was performed with the aim of characterizing the pept... |
Cell-free transcription and translation (TXTL) systems have emerged as a powerful tool for testing genetic regulatory elements and circuits. Cell-free prototyping can dramatically accelerate the design-build-test cycle of new functions in synthetic biology, in particular when linear DNA templates are used. |
Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses. |
We show that the relative Auslander-Buchweitz context on a triangulated category $\T$ coincides with the notion of co-$t$-structure on certain triangulated subcategory of $\T$ (see Theorem \ref{M2}). In the Krull-Schmidt case, we stablish a bijective correspondence between co-$t$-structures and cosuspended, precoverin... |
Given a functor $p:E \rightarrow B$ and an object $e \in E$ , we define a \emph{displacement} of $e$ along a morphism $\varepsilon: p(e) \rightarrow b$, as a map $e \rightarrow \nabla_\varepsilon(e)$ satisfying a universal property analogue to that of a \emph{cocartesian lifting} (pushforward) \emph{à la} Bénabou-Groth... |
Equivariant monoids are very important objects in many branches of mathematics: they combine the notion of multiplication and the concept of a group action. In this paper we will construct categories which encode the structure borne by monoids with a group action by combining the theory of PROPs and PROBs with the the... |
We provide a definition of enrichment that applies to a wide variety of categorical structures, generalizing Leinster's theory of enriched $T$-multicategories. As a sample of newly enrichable structures, we describe in detail the examples of enriched monoidal categories and enriched double categories, with a focus... |
Using a categorial version of Fraïssé's theorem due to Droste and Göbel, we derive a criterion for a comma-category to have universal homogeneous objects. <br>As a first application we give new existence result for universal structures and for \omega-categorical universal structures. |
In this paper we present the construction of a skeletal diagram category, which we call the square with bands category. This category extends the Temperley-Lieb (TL) category, where morphisms now include diagrams of embedded curves on (possibly) non-orientable bounded surfaces, and involves three parameters associated... |
In this note we study the local projective model structure on presheaves of complexes on a site, i.e. we describe its classes of cofibrations, fibrations and weak equivalences. In particular, we prove that the fibrant objects are those satisfying descent with respect to all hypercovers. |
As far as we know no notion of concreteness for fibrations exists. We introduce such a notion and discuss some basic results about it. |
The goal of this article is to describe several presentations of the infinity category of algebras over some monad on the infinity category of chain complexes. |
We prove that for certain monoidal (Quillen) model categories, the category of comonoids therein also admits a model structure. |
The abelian category of tetramodules over an associative bialgebra $A$ is related with the Gerstenhaber-Schack (GS) cohomology as $Ext_\Tetra(A,A)=H_\GS(A)$. We construct a 2-fold monoidal structure on the category of tetramodules of a bialgebra. |
The category Rel of sets and relations intimately ties the notions of function, partial multivalued function, and direct image under a function through the description of Rel as the Kleisli category of the covariant power set functor on Set. We present a suitable framework to obtain a similar relationship between the ... |
We study localizations of infinity categories that remain localizations after any base change. |
A Morita class of symmetric special Frobenius algebras A in the modular tensor category of a chiral CFT determines a full CFT on oriented world sheets. For unoriented world sheets, A must in addition possess a reversion, i.e. an isomorphism from A^opp to A squaring to the twist. |
Motivated by some problems proposed by Cuadra and Simson related to flat objects in finitely accessible Grothendieck categories, we study flatness in the more general setting of finitely accessible additive categories. For such category $\mathcal{A}$, we characterize when $\mathcal{A}$ is preabelian and abelian. |
Suppose an extension map $U\colon \mathbb{T}_1 \to \mathbb{T}_0$ in the 2-category $\mathfrak{Con}$ of contexts for arithmetic universes satisfies a Chevalley criterion for being an (op)fibration in $\mathfrak{Con}$. If $M$ is a model of $\mathbb{T}_0$ in an elementary topos $\mathcal{S}$ with nno, then the classifier... |
As an example of the categorical apparatus of pseudo algebras over 2-theories, we show that pseudo algebras over the 2-theory of categories can be viewed as pseudo double categories with folding or as appropriate 2-functors into bicategories. Foldings are equivalent to connection pairs, and also to thin structures if ... |
Involutive category theory provides a flexible framework to describe involutive structures on algebraic objects, such as anti-linear involutions on complex vector spaces. Motivated by the prominent role of involutions in quantum (field) theory, we develop the involutive analogs of colored operads and their algebras, n... |
This paper is devoted to the more elementary aspects of the contramodule story, and can be viewed as an extended introduction to the more technically complicated <a href="https://arxiv.org/abs/1503.05523" data-arxiv-id="1503.05523" class="link-https">arXiv:1503.05523</a>. Reduced cotorsion abelian groups form an abeli... |
We give an algebraic characterisation of ordered groupoids, namely, we show that there is a categorical isomophism between the category of ordered groupoids and the category of $D$-inverse constellations. Here constellations are partial algebras in the sense that they possess a partial product, and a unary operation $... |
As composites of constant, (co)product, identity, and powerset functors, Kripke polynomial functors form a relevant class of $\mathsf{Set}$-functors in the theory of coalgebras. The main goal of this paper is to expand the theory of limits in categories of coalgebras of Kripke polynomial functors to the context of qua... |
We study when the heart of a t-structure in a triangulated category $\mathcal{D}$ with coproducts is AB5 or a Grothendieck category. If $\mathcal{D}$ satisfies Brown representability, a t-structure has an AB5 heart with an injective cogenerator and coproduct-preserving associated homological functor if, and only if, t... |
In this note some recent developments in the study of homology in semi-abelian categories are briefly presented. In particular the role of protoadditive functors in the study of Hopf formulae for homology is explained. |
A fusion category is called transparent if the associator involving any invertible object is the identity map. For the Haagerup-Izumi fusion rings with $G = \mathbb{Z}_{2n+1}$ (the $\mathbb{Z}_3$ case is the Haagerup fusion ring with six simple objects), the transparent ansatz reduces the number of independent $F$-sym... |
Algebraic weak factorisation systems (AWFS) refine weak factorisation systems by requiring that the assignations sending a map to its first and second factors should underlie an interacting comonad--monad pair on the arrow category. We provide a comprehensive treatment of the basic theory of AWFS---drawing on work of p... |
Topos properties of the category of covering groupoids over a fixed groupoid are discussed. A classification result for connected covering groupoids over a fixed groupoid analogous to the fundamental theorem of Galois theory is given. |
The Verdier quotient $\mathcal{T}/\mathcal{S}$ of a triangulated category $\mathcal{T}$ by a triangulated subcategory $\mathcal{S}$ is defined by a universal property with respect to triangulated functors out of $\mathcal{T}$. However, $\mathcal{T}/\mathcal{S}$ is in fact a localization of $\mathcal{T}$, i.e., it is o... |
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