The results of a long-term study (2006–2024) on the phenology of 25 species of herbaceous plants, represented by 33 accessions from natural populations in the Russian Far East (Primorye, Sakhalin, and the Southern Kurils), under conditions of the forest-steppe of Western Siberia (Novosibirsk) are presented. The study has revealed the features of seasonal rhythms for most of the accessions: spring growth is observed in the early to middle period (April–first decade of May) and the onset of flowering is timed to the summer period (June–mid-July), with a phenorhythmotype classified as spring–summer-green. Therefore, with respect to the primary rhythmic characteristics, the Far Eastern accessions correspond to herbaceous perennials of the regional flora. At the same time, the complete and regular seasonal cycle as an indicator of biological sustainability is observed in 16 accessions (48

The results of a phenological study of 78 species of perennial plants from biomorphological groups of chamaephytes, hemicryptophytes, and geophytes over a 20-year period (1996–2015) are discussed. Against the background of air temperature and precipitation changes of the warm season in Novosibirsk, the timing shift in phenological events have been analyzed using calculated linear trends. It is found that the trends for species groups are multidirectional and vary significantly in magnitude. At the same time, most of the shifts in phenology are due, not to trends, but to the interannual variability of climatic indicators.

Обсуждаются результаты 20-летнего исследования (1996-2015) фенологии 78 видов многолетних растений в условиях западносибирской лесостепи. На фоне рассчитанных метеорологических трендов теплого сезона года в Новосибирске проанализировано смещение времени фенологических событий у отдельных видов и экологических групп путем построения линейных трендов. Установлено, что сроки начала вегетации у подавляющего большинства многолетников запаздывали (+3 … +7 дней), а сроки окончания вегетации изменились неодинаково (-4 … +1), при этом длительность вегетации уменьшилась во всех группах. Продолжительность префлорального периода существенно сократилась (-6 … -9 дней) за счет более позднего начала вегетации и более раннего начала цветения (-1 … -2 дня). Тренды плодоношения различались по направлению и величине. Темпы сезонного развития видов в целом ускорились за рассматриваемый период. Тренды описывают 6-32 % изменений фенологических событий в экологических группах. The results on the phenology study of 78 species of perennial plants over 20-year period 1996-2015 in the Western Siberia forest-steppe are discussed. Against the background of the detected meteorological trends of the warm season in Novosibirsk, the timing shift in phenological events of individual species and their ecological groups were analyzed using linear trends. It was found that vegetation start in the vast majority of perennials delayed on +3 … +7 days, and the terms of vegetation end changed differently within -4 … +1 days, while the duration of vegetation decreased in all groups. The duration of prefloral period significantly decreased by -6 … -9 days, due to the later vegetation start and an earlier start of flowering on -1 … -2 days. Fruiting trends are differed in direction and magnitude. The rate of seasonal development of the species generally accelerated over the observation period. Trends describe 6-32 % of phenological changes in ecological groups.

The structure and paramagnetic properties of the [Dy(H2O)n(CyDTA)]– complex are studied by 1H NMR using the analysis of paramagnetic shifts and spin-spin relaxation rates for an ab initio structural model. It is shown that significant temperature-dependent spectral line broadening is due to the Curie-spin contribution to the paramagnetic spin-spin relaxation rate enhancement. The complex demonstrates conformational, kinetic, and thermodynamic stability in the temperature range from 278 K to 368 K. The maximum temperature sensitivity of chemical shifts d(δexp)/dT is equal to 0.44 ppm/K. Due to its thermodynamic and conformational stability, this compound may be prospective for the design of thermally sensitive NMR probes in aqueous media.

The processes of spin-crossover (SCO) transition in the solid phase and in the solution for complexes of [Fe(HC(Pz)(3))(2)](CF3SO3)(2) and [Fe(HC(Pz)(3))(2)]SiF6 were studied by UV-vis-spectrometry and NMR methods. According to NMR, the both complexes in solution showed the monotonic decrease in the fraction of the low-spin (LS) state and the increase in the fraction of the high-spin (HS) state when the temperature increases from 295 to 360 K. The observed chemical shifts and signal half-widths change significantly on temperature, despite the fact that the fraction of the HS form increases with rising temperature not so sharp as in the solid phase. The increased in temperature sensitivity of the observed chemical shifts in comparison with the temperature sensitivity of the "pure" HS and LS forms is caused by a growth in the relative population of the HS form with temperature rising. The significant temperature dependences of the observed chemical shifts and signal half-widths are suggested to use for temperature control in liquid media using NMR and MRI.

Методом 1Н ЯМР исследовано строение и парамагнитные свойства комплекса [Dy(H2O)n(CyDTA)]- с помощью методик, основанных на анализе парамагнитных сдвигов и скоростей спин-спиновой релаксации, с применением полученной ab initio структурной модели. Обнаружено, что существенное температурно-зависимое уширение сигналов спектров обусловлено наличием Кюри-спинового вклада в увеличение скорости спин-спиновой релаксации. Комплекс характеризуется конформационной стабильностью, кинетической и термодинамической устойчивостью в диапазоне температур от 278 K до 368 K. Максимальная температурная чувствительность химических сдвигов d(δexp)/dT оказалась равной 0,44 м.д./K. Благодаря термодинамической устойчивости и конформационной стабильности, данное соединение может представлять интерес для дизайна термочувствительных ЯМР-зондов в водных средах.

Data on the seasonal development of 78 species of perennial plants in the forest-steppe conditions of Western Siberia have been generalized over a 20-year period (1996–2015) due to changes in the regional climate. It is demonstrated that the meteorological parameters of the warm season of the year in Novosibirsk have undergone significant changes: the average daily air temperature has increased by 0.16°C, the growing season has lengthened by 12 days, and the active vegetation period of plants at temperatures above 10°C has lengthened by 8 days. The correlations of the time of regrowth phenophases and the beginning of flowering of perennials with the data of snow-cover disappearance, dates of transition of average daily air temperatures through 5 and 10°С upward, and sums of these temperatures are detected. Using linear phenological trends, a delay within 2–6 days of the beginning of the vegetation and the advanced beginning of flowering (except for early summer species) by 2–10 days are established. Shortening the duration of prefloral period from 5 to 24 days indicates an acceleration in the rate of the development of perennials against the background of the detected meteorological trends. A change in the duration of vegetation is significant in spring–autumn green and spring–summer–winter green species (10 and 12 days, respectively). Low values of determination coefficient for most trends R2 < 0.06 demonstrated that changes in the phenology of species are mainly caused by interannual variability.

The present work is devoted to the phenology of individual flowering and the construction of structure-dynamic models of this process on its basis. The results of the study of the flowering phenology of Campanula bononiensis, C. sarmatica and Platycodon grandiflorus are presented. The data obtained characterize both the phenological (time and duration of flowering, lifespan of individual flowers) and structural features (degree of branching of the inflorescence, length of floral axes, number of flowers, order of their blooming) that describe the flowering of a monocarpic shoot. Inflorescences of the species are elongated and multiflorous, of the compound type inherent for Campanulaceae, and characterized by a high variability of all structural features. Observation data were processed by standard statistical methods and used to construct stochastic computer models of flowering shoots, while omissions in data were restored by using the maximum likelihood method. Flowering patterns of the species, due to differences in phenological and structural features, have been revealed. It has been shown that flowering curves depend on the synchrony in the flowers blooming on the main (first-order) axis and lateral (second-order) axes. C. bononiensis has one asymmetrical peak with a broadening on the left, achieved with the simultaneous blooming of flowers in the upper and lower parts of the main axis and on lateral axes in the middle part of the inflorescence, where the first-order flowers have already finished blooming (they provided the broadening). Flowering curves for C. sarmatica and P grandiflorus are bimodal, with the first peak being due to the flowers blooming on the main axis and the second one on lateral axes. The constructed models reproduce the patterns of individual flowering well, with natural variability, and can be used to simulate the flowering of a group of individuals (population), for example, in landscape design. In combination with visualization tools, they can be used for augmenting plant phenotyping datasets with rendered images of synthetic plants for the purpose of training neural networks in this field.

The present work is devoted to the phenology of individual flowering and the construction of structure-dynamic models of this process on its basis. The results of the study of the flowering phenology of Campanula bononiensis, C. sarmatica and Platycodon grandiflorus are presented. The data obtained characterize both the phenological (time and duration of flowering, lifespan of individual flowers) and structural features (degree of branching of the inflorescence, length of floral axes, number of flowers, order of their blooming) that describe the flowering of a monocarpic shoot. Inflorescences of the species are elongated and multiflorous, of the compound type inherent for Campanulaceae, and characterized by a high variability of all structural features. Observation data were processed by standard statistical methods and used to construct stochastic computer models of flowering shoots, while omissions in data were restored by using the maximum likelihood method. Flowering patterns of the species, due to differences in phenological and structural features, have been revealed. It has been shown that flowering curves depend on the synchrony in the flowers blooming on the main (first-order) axis and lateral (second-order) axes. C. bononiensis has one asymmetrical peak with a broadening on the left, achieved with the simultaneous blooming of flowers in the upper and lower parts of the main axis and on lateral axes in the middle part of the inflorescence, where the first-order flowers have already finished blooming (they provided the broadening). Flowering curves for C. sarmatica and P grandiflorus are bimodal, with the first peak being due to the flowers blooming on the main axis and the second one on lateral axes. The constructed models reproduce the patterns of individual flowering well, with natural variability, and can be used to simulate the flowering of a group of individuals (population), for example, in landscape design. In combination with visualization tools, they can be used for augmenting plant phenotyping datasets with rendered images of synthetic plants for the purpose of training neural networks in this field.

An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.

Mass spectrometry is a physical method, which can be applied to the investigation of proteomes of different organisms. It allows us both to solve the problem of identification of biological macromolecules and to sequence peptide chains in cases where information on the genomes is scarce or absent. Currently, there are many software programs to support research in this area. Nevertheless, in spite of all efforts, there is little progress in the development of programs able to solve the problem for de novo sequencing of cyclic peptides, which are most effective antibiotics, antitumor agents, immunosuppressants, toxins, and a vast number of nonribosomal peptides with unknown functions. In this paper, an effective algorithm for solving the problem of de novo sequencing cyclic peptides is proposed. The algorithm allows us to reconstruct sequences of lengths up to 160 amino acid residues.

The method of mass spectrometry is one of physical methods of proteome study in different organisms; it allows us to solve both problems of biological macromolecule identification and sequencing of peptide chains in cases in the absence of or limited information about genomes. At present, there are many computer programs for supporting the studies in this field. Nevertheless, in spite of the high activity, there is only insignificant progress in creating programs allowing us to solve problems of de novo sequencing for cyclic peptides, which include the most efficient antibiotics, antitumor agents, immunosuppressants, toxins, and many peptides with unknown functions synthesized in the cell by a nonribosomal pathway. An efficient algorithm for solving the problem of cyclic peptide sequencing, which allows us to restore sequences of large length of up to 160 amino acid residues, was suggested.

Classification of existent theoretical approaches for investigating protein thermal stability is performed. Computer simulations allow to fully estimate micro- and macro properties of the molecules. But those approaches are limited in accuracy and therefore require certain improvements e.g. making them to allow for molecular charge distribution. Also promising methods are those dealing with rigid regions of proteins. They do not require a huge amount of computations and allow to directly determine changes in molecular structure flexibility caused by mutated amino acid residues. But using the only structure it is impossible to explicitly estimate an effect of solvent and its thermodynamical properties.

The thermal stability of several barnase mutants has been studied by the λ dynamics method. The method is implemented in the MOLKERN software package. Mutations involving amino acids with nonzero charge are chosen for the study, because in this case λ dynamics produces results differing dramatically (>10 kJ/mol) from experimental data in nearly one-fourth of cases. A modification of λ potentials is proposed to take into account charge changes. The Net-Q method is another tool to make charge distributions for charged amino acids reliable. The results obtained for the R72G mutation show better agreement with experimental values than those obtained by other authors.

Аннотация.Представлен программный комплекс L-MOLKERN для расчетов разностей свободных энергий молекулярных комплексов методом λдинамики.Для уточнения расчетов разностей свободных энергий

Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short-range inter-atomic potentials. These algorithms are based on the Verlet table (VT) or celllinked list (CLL) methods. In this work, we have analyzed some features of these methods and found that for a dense system, such as water, the CLL significantly outperforms the VT with respect to both the memory size and the number of data transfer operations and can be efficiently used for parallel implementation. A new technique for parallelizing short-range interactions referred to as dynamic spatial decomposition is proposed for the CLL approach. It has been shown that the CLL method, especially its version improved by P. Gonnet, outperforms the VT by up to 40% or more in parallel SIMD implementations in spite of a large number of unnecessary inter-particle distance calculations. The efficiency gain is achieved due to the fact that the CLL is more suitable for modern multi-core SIMD processors. The methods were tested in the MOLKERN simulation software.

The library of software components MOLKERN is designed to construct efficient programs (with linear computational complexity) for modeling, optimization, and analysis of spatial structures of proteins, cofactors, ligands, and their complexes and computation of their physical properties. The interactions between atoms and molecules are taken into account within the force field method. The library is realized in C++ using static polymorphism technology. The library utilizes STL and BOOST libraries and contains a number of software components for parallel computation using the MPI technology. The library can be used under Windows and Linux.

Our earlier suggestion that the G245C mutation in p53 generates an additional zinc binding site, overlapping with the normal zinc binding site, has been supported by molecular modeling. The energy of interaction between a zinc ion and the new site in the G245 mutant is comparable to that for the normal site in wild-type p53. The presence of the additional site in the mutant can distort its conformation when it interacts with DNA. Effects of other mutations on the energy of zinc binding to the normal site have been calculated.

A relationship between the functional significance of individual amino acid residues of the p53 protein, their positions in the protein structure, and the mode of evolution of the codons corresponding to these residues has been established. A phylogenetic analysis of the coding sequences of the gene of p53 from 32 vertebrate species has been performed. It was found that those codons undergo selection that affect the efficiency of binding of protein p53 as a transcription factor. It was shown that the frequency of occurrence of generative mutations maintaining the normal function of the protein in conservative codons differs statistically significantly from the frequency of occurrence in the same codons of mutations with the effects of loss and acquisition of the function, and the negatively dominant effect. The phylogenetic analysis and molecular dynamics modeling made it possible to obtain evidence for the functional significance of the G245 residue for which the appearance of the binding site for Zn2+ in the case of the substitution G245G has previously been proposed.

Motivation: At present, there are abundant experimental data concerning associations between the mutations in the p53 protein and cancer. Not of all the molecular mechanisms underlying the impairment of p53 function are known.Results: We support here our previous assumption that G245C mutations can give rise to an additional Zn binding site in the immediate vicinity to the functionally significant binding site (Ivanisenko et al., 2005). We demonstrated here that the interaction energy of the Zn ion in the G245C mutant with the de novo arisen site is commensurate with the interaction energy in the wild-type p53. The presence of an additional site in the mutant can damage p53 conformation upon interaction with DNA. Also, using molecular mechanics, we calculated the effects of certain other mutations on the zinc interaction energy with the normal site.