Competitive pathways for peptide deamidation

Asparagine (Asn) residues spontaneously – yet non-enzymatically – deamidate to form aspartate under physiological conditions, causing time-dependent changes in the conformation of proteins, limiting their lifetime [1]. The 'molecular clocks' hypothesis [2], suggests that deamidation is a biological molecular timing mechanism that could be set to any desired time interval by genetic control of the protein structure and the immediate environment of the Asn residue. The fact that deamidation occurs over a wide range of biologically relevant time intervals suggests that different mechanisms may be at play. To date deamidation is believed to occur over a succinimide-mediated pathway [3]. A novel route leading to the succinimide intermediate via tautomerization of the Asn side chain amide functionality was recently proposed [4,5]. The current study introduces a new 'competing' route for the deamidation of asparagine residues. The aim is to comparatively analyze the feasibility of this new mechanism against the traditional succinimide route, taking into account the catalytic effect of the solvent environment. For this purpose, QM dynamics and meta-dynamics calculations were performed on a model peptide placed in a periodic water box. These results will identify the lowest energy pathway for asparagine deamidation and will serve as a stepping stone for QM/MM calculations of Asn deamidation in proteins

Elucidation of the acetamide hydrolysis mechanism using QM metadynamics simulations

The reaction mechanism for the hydrolysis of amide bonds is a much debated topic in literature. This is not surprising when considering the variety of biologically significant domains in which this reaction is of interest, ranging from peptide bonds to protein side chain degradation. For instance, asparagine (Asn) and glutamine (Gln) residues are known to undergo spontaneous nonenzymatic deamidation in water to form aspartic acid and glutamic acid residues under physiological conditions. Deamidation could be the result of a hydrolysis reaction, either via a concerted or a stepwise mechanism. Gas phase calculations have shown that explicit water molecules play an important role in this reaction, but to date, no simulations of hydrolysis pathways using a periodic water model have been performed. In this work, we perform quantum mechanical metadynamics simulations on the hydrolysis of acetamide as a model compound for Asn or Gln. The periodic simulation cell consists of one acetamide molecule and 90 water molecules in a cubic 15 Å box. From all previously suggested pathways and a new, alternative route, the most competitive pathway can be identified. These results give a clearer insight in deamidation processes proteins and polypeptides and show that an adequate description of the natural surroundings the active species is necessary for obtaining a realistic image of biological processes

Ab initio evaluation of metalated 3-halo-1-azaallylic anions as synthetic building blocks

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Тантризм в контексте теории мистического опыта просветления

У статті досліджується індійський тантризм і робиться висновок, що він постає іманентним містичним напрямом, який стверджує тотожність індивідуального та абсолютного духовного начал. Він відноситься до холічного містицизму, що закликає до прийняття матеріального буття у всіх його аспектах. Основними методами просвітлення у тантризмі є медитація і різноманітні види йоги тіла (пранаяма, асана, сексуальна йога). Не використовується в цій формі містичного досвіду такий метод як бхакті, почуттєво-емоційне служіння Абсолюту шляхом віри та любові.В статье исследуется индийский тантризм и делается вывод, что он является имманентным мистическим направлением, которое утверждает тождественность индивидуального и абсолютного духовного начал. Он относится к холическому мистицизму, который призывает к приятию всех аспектов материального бытия. В качестве основных методов просветления в тантризме используется медитация и разнообразные виды йоги тела (пранаяма, асана, сексуальная йога). Практически не используется в данной форме мистического опыта такой метод как бхакти, чувственно-эмоциональное служение Абсолюту путем любви и веры.The article studies Indian tantrism and the conclusion can be made that it is an immanent mystical policy which affirms the identity of individual and absolute origins. It has to do with the whole mysticism which appeals to accept all the aspects of the material being. As the main methods of enlightening tantrism uses meditation and different kinds of body yoga (pranayama, asana, sexual yoga). Such method as bhakti, the sensual and emotional service to the Absolute by means of love and faith, is not practically used in this form of the mystical experience

Diastereoselective Aldol reaction of Zincated 3-Chloro-3-methyl-1-azaallylic anions as key step in the synthesis of 1,2,3,4-Tetrasubstituted 3-Chloroazetidines

Zincated 3-chloro-3-methyl-1-azaallylic anions undergo a stereoselective aldol addition across aromatic aldehydes and subsequent mesylation to produce syn alpha-chloro-beta-mesyloxyketimines, which were isolated in 80-84% yield and high diastereomeric excess (dr > 97/3) after purification via flash chromatography. The syn alpha-chloro-beta-mesyloxyketimines were further stereoselectively reduced to give stereochemically defined 3-aminopropyl mesylates, which were cyclized to 1,2,3,4-tetrasubstituted 3-chloroazetidines containing three contiguous stereogenic centers. DFT calculations on the key aldol addition revealed the presence of a highly ordered bimetallic six-membered twist-boat-like transition state structure with a tetra-coordinated metal cyclic structure. DFT calculations revealed that chelation of both zinc and lithium cations in the transition state structure leads to the experimentally observed high syn diastereoselectivity of aldol reactions

Solvent effects in chemical, biochemical and polymerization reactions, studied with static and dynamic molecular modeling techniques

Ab initio moleculaire modelleringstechnieken worden reeds lange tijd met succes toegepast voor de beschrijving van de kinetiek en mechanismen van chemische reacties in de gasfase. Toch zijn er veel reacties die doorgaan in oplossing en waarvoor er experimentele aanwijzingen zijn dat het solvent of oplosmiddel een grote invloed kan uitoefenen op de reactie. De theoretische studie naar de effecten van deze oplosmiddelen op chemische reacties laat toe om inzicht te verkrijgen in deze processen. Deze theoretische beschrijving is mogelijk door de ontwikkeling van diverse modellen en de enorme toename in computerkracht gedurende de voorbije jaren. In dit proefschrift werden de meest gangbare modellen toegepast op 3 verschillende chemische systemen uit de organische chemie, de polymeerchemie en de biochemie. Op die manier kunnen er enerzijds algemene besluiten getrokken worden over de prestatie van de modellen en anderzijds kan de invloed van de solventomgeving op de verschillende reacties onderzocht worden. Afhankelijk van het solvent en de bestudeerde reactie dienen andere modellen gebruikt te worden om een goed kwalitatief, kwantitatief en structureel realistisch beeld te krijgen van het bestudeerde systeem. Dit doctoraatswerk geeft een overzicht van de factoren die belangrijk zijn bij de selectie van het model en laat daardoor toe om op een gefundeerde wijze de geschikte methodologie te kiezen

QM metadynamics study on asparagine deamidation in proteins

Asparagine (Asn) residues spontaneously deamidate to form aspartate under physiological conditions, causing time-dependent changes in the conformation of proteins, limiting their lifetime. The 'molecular clocks' hypothesis [1], suggests that deamidation is a biological molecular timing mechanism that could be set to any desired time interval by genetic control of the protein structure. To date deamidation is believed to occur over a succinimide-mediated pathway. Concerted and stepwise pathways leading to the succinimide intermediate were previously explored with the inclusion of explicit water molecules [2,3]. The current study introduces a new 'competing' route for the deamidation of asparagine residues. The aim is to comparatively analyze the feasibility of this new mechanism against the traditional succinimide route, taking into account the catalytic effect of the solvent environment via QM dynamics and meta-dynamics calculations on a model peptide placed in a periodic water box. These results will identify the lowest energy pathway for asparagine deamidation and will serve as a stepping stone for calculations of Asn deamidation in proteins