Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules.

Computer simulations of biomolecules such as molecular dynamics often suffer from insufficient sampling. Due to limited computational resources, insufficient sampling prevents obtaining proper equilibrium distributions of observed properties. To deal with this problem, we proposed a simulation protocol for efficient resampling of collected off-equilibrium trajectories.

Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x-ray reference structures as a prediction benchmark.

Proteins are naturally formed by domains edging their functional and structural properties. A domain out of the context of an entire protein can retain its structure and to some extent also function on its own. These properties rationalize construction of artificial fusion multidomain proteins with unique combination of various functions.

Modern and prebiotic amino acids support distinct structural profiles in proteins.

The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the 'late' amino acids (such as Arg, Lys, His, Cys, Trp and Tyr) belong to essential catalytic and structure-stabilizing residues. How (or if) early proteins could sustain an early biosphere has been a major puzzle.

TRPM5 Channel Binds Calcium-Binding Proteins Calmodulin and S100A1.

Melastatin transient receptor potential (TRPM) channels belong to one of the most significant subgroups of the transient receptor potential (TRP) channel family. Here, we studied the TRPM5 member, the receptor exposed to calcium-mediated activation, resulting in taste transduction. It is known that most TRP channels are highly modulated through interactions with extracellular and intracellular agents.

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures.

Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.

Characterization of AMBN I and II Isoforms and Study of Their Ca-Binding Properties.

Ameloblastin (Ambn) as an intrinsically disordered protein (IDP) stands for an important role in the formation of enamel-the hardest biomineralized tissue commonly formed in vertebrates. The human ameloblastin (AMBN) is expressed in two isoforms: full-length isoform I (AMBN ISO I) and isoform II (AMBN ISO II), which is about 15 amino acid residues shorter than AMBN ISO I. The significant feature of AMBN-its oligomerization ability-is enabled due to a specific sequence encoded by exon 5 present at the N-terminal part in both known isoforms.

Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function.

Constantly increasing attention to bioengineered proteins has led to the rapid development of new functional targets. Here we present the biophysical and functional characteristics of the newly designed CaM/AMBN-Ct fusion protein. The two-domain artificial target consists of calmodulin (CaM) and ameloblastin C-terminus (AMBN-Ct).

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Intrinsically disordered proteins (IDPs) represent a distinct class of proteins and are distinguished from globular proteins by conformational plasticity, high evolvability and a broad functional repertoire. Some of their properties are reminiscent of early proteins, but their abundance in eukaryotes, functional properties and compositional bias suggest that IDPs appeared at later evolutionary stages. The spectrum of IDP properties and their determinants are still not well defined.

Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective.

By combining bioinformatics with quantum-chemical calculations, we attempt to address quantitatively some of the physical principles underlying protein folding. The former allowed us to identify tripeptide sequences in existing protein three-dimensional structures with a strong preference for either helical or extended structure. The selected representatives of pro-helical and pro-extended sequences were converted into "isolated" tripeptides-capped at N- and C-termini-and these were subjected to an extensive conformational sampling and geometry optimization (typically thousands to tens of thousands of conformers for each tripeptide).

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation.

Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. We conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation.

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins.

Domains are distinct units within proteins that typically can fold independently into recognizable three-dimensional structures to facilitate their functions. The structural and functional independence of protein domains is reflected by their apparent modularity in the context of multi-domain proteins. In this work, we examined the coupling of evolution of domain sequences co-occurring within multi-domain proteins to see if it proceeds independently, or in a coordinated manner.

[Life threatening manifestations of lupus and antiphospholipid syndrome in internal medicine].

The clinical picture of systemic lupus and antiphospholipid syndrome is remarkably varied and disease manifestations are commonly very heterogeneous. Relatively often both diseases are associated with severe, acute and life threatening manifestations, which places demands on the knowledge of differential diagnostics and experience of the physicians. This article deals with the serious and mostly acute impairment of cardiovascular, respiratory, renal, gastrointestinal, hematopoietic or nervous systems, briefly discusses the acute pregnancy complication and summarizes the basic therapeutic option.

Cardiac amyloidosis: from clinical suspicion to morphological diagnosis.

Amyloidosis is a heterogeneous group of diseases characterised by extracellular accumulation of amyloid in various tissues and organs of the body, leading to alteration and destruction of tissues. Heart involvement is the most important prognostic factor in patients with systemic amyloidosis and the diagnosis and typing of amyloid must be made properly. The clinical picture shows congestive heart failure with predominant right-sided heart failure symptoms in fully developed disease, various types of arrhythmias and characteristic electrocardiography and echocardiography findings.

Focused conformational sampling in proteins.

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system.

Random protein sequences can form defined secondary structures and are well-tolerated in vivo.

The protein sequences found in nature represent a tiny fraction of the potential sequences that could be constructed from the 20-amino-acid alphabet. To help define the properties that shaped proteins to stand out from the space of possible alternatives, we conducted a systematic computational and experimental exploration of random (unevolved) sequences in comparison with biological proteins. In our study, combinations of secondary structure, disorder, and aggregation predictions are accompanied by experimental characterization of selected proteins.

Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip.

The growth of amyloid fibrils from Aβ peptide, one of the key pathogenic players in Alzheimer's disease, is believed to follow a nucleation-elongation mechanism. Fibril elongation is often described as a "dock-lock" procedure, where a disordered monomer adsorbs to an existing fibril in a relatively fast process (docking), followed by a slower conformational transition toward the ordered state of the template (locking). Here, we use molecular dynamics simulations of an ordered pentamer of Aβ42 at fully atomistic resolution, which includes solvent, to characterize the elongation process.

Amino Acid Interaction (INTAA) web server.

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.

Emergency situations in rheumatology with a focus on systemic autoimmune diseases.

Background And Aim: Rheumatic diseases are commonly considered chronic conditions. However, acute manifestations can be very severe and represent a diagnostic problem. Examples are systemic lupus erythematosus with acute flare, glomerulonephritis, CNS disorders and catastrophic antiphospholipid syndrome, scleroderma with interstitial lung disease, pulmonary hypertension and renal crisis and polyangiitis with alveolar haemorhage and acute respiratory failure.

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.

Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure.

Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

Fluorinated alcohols such as 2,2,2-trifluoroethanol (TFE) are among the most frequently used cosolvents in experiment studies of peptides. They have significant effects on secondary structure and a particularly strong promotion of α-helix is induced by TFE. In this study we validated recently proposed force field parameters for TFE in molecular dynamics simulations with two model peptides-alanine-rich AK-17 and antimicrobial peptide halictine-1 (HAL-1).

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.

Amino acid sequence and environment are the most important factors determining the structure, stability and dynamics of proteins. To evaluate their roles in the process of folding, we studied a retroversion of the well-described Trp-cage miniprotein in water and 2,2,2-trifluoroethanol (TFE) solution. We show, by circular dichroism spectroscopy and nuclear magnetic resonance (NMR) measurement, that the molecule has no stable structure under conditions in which the Trp-cage is folded.

Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions.

We present a novel force field model of 2,2,2-trifluoroethanol (TFE) based on the generalized AMBER force field. The model was exhaustively parametrized to reproduce liquid-state properties of pure TFE, namely, density, enthalpy of vaporization, self-diffusion coefficient, and population of trans and gauche conformers. The model predicts excellently other liquid-state properties such as shear viscosity, thermal expansion coefficient, and isotropic compressibility.

Critical Assessment of Current Force Fields. Short Peptide Test Case.

The applicability of molecular dynamics simulations for studies of protein folding or intrinsically disordered proteins critically depends on quality of energetic functions-force fields. The four popular force fields for biomolecular simulations, CHARMM22/CMAP, AMBER FF03, AMBER FF99SB, and OPLS-AA/L, were compared in prediction of conformational propensities of all common proteinogenic amino acids. The minimalistic model of terminally block amino acids (dipeptides) was chosen for assessment of side chain effects on backbone propensities.

Gyration- and inertia-tensor-based collective coordinates for metadynamics. Application on the conformational behavior of polyalanine peptides and Trp-cage folding.

Effective simulations of proteins, their complexes, and other amino-acid polymers such as peptides or peptoids are critically dependent on the performance of the simulation methods and their ability to map the conformational space of the molecule in question. The most important step in this process is the choice of the coordinates in which the conformational sampling will be executed and their uniqueness regarding the capability to unambiguously determine the energy minimum on the free-energy hypersurface. In the presented study, we show that metadynamics and chosen collective coordinates-the principal moments of the tensors of gyration and inertia, the principal radii of gyration around the principal axes, asphericity, acylindricity, and anisotropy-can be used as a powerful combination to map the conformational space of peptides and proteins.

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure.