Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design

2017 ◽  
Vol 38 (28) ◽  
pp. 2396-2410 ◽  
Author(s):  
Francesco Villa ◽  
David Mignon ◽  
Savvas Polydorides ◽  
Thomas Simonson
Keyword(s):  
Protein Design ◽  
Many Body ◽  
Acid Base ◽  
Generalized Born

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

2011 ◽  
Vol 79 (12) ◽  
pp. 3448-3468 ◽  
Author(s):  
Savvas Polydorides ◽  
Najette Amara ◽  
Caroline Aubard ◽  
Pierre Plateau ◽  
Thomas Simonson ◽  
...  
Keyword(s):  
Protein Design ◽  
Trna Synthetase ◽  
Computational Protein Design ◽  
Model Application ◽  
Generalized Born ◽  
Solvent Model

Predicting the Acid/Base Behavior of Proteins: A Constant-pH Monte Carlo Approach with Generalized Born Solvent

2010 ◽  
Vol 114 (32) ◽  
pp. 10634-10648 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Savvas Polydorides ◽  
Georgios Archontis ◽  
Thomas Simonson
Keyword(s):  
Monte Carlo ◽  
Acid Base ◽  
Generalized Born ◽  
Monte Carlo Approach ◽  
Constant Ph

A COMPUTER SIMULATION STUDY ON LEWIS ACID–BASE INTERACTIONS AND COOPERATIVE C-H⋯O WEAK HYDROGEN BONDING IN VARIOUS CO2 COMPLEXES

2011 ◽  
Vol 10 (04) ◽  
pp. 483-508 ◽  
Author(s):  
XINGMEI ZHANG ◽  
XIAOLONG HAN ◽  
WENHAO XU
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Monte Carlo Simulations ◽  
Ab Initio ◽  
Lewis Acid ◽  
Many Body ◽  
Acid Base ◽  
Base Interaction ◽  
Many Body Interactions ◽  
Acid Base Interaction

The Lewis acid–base interaction and cooperative C-H⋯O weak hydrogen bonding have been widely suggested as two key factors in the solubility of CO2 -philic materials. In this work, both ab initio and Monte Carlo simulations were performed to investigate the properties of the two important interactions between CO2 and several common organic molecules. Binding energies, geometries and charge transfer were calculated by ab initio method, showing that the mutual enhancement between the two sorts of interactions plays an important role in the stability of the CO2 complexes. Monte Carlo simulations were employed to investigate the effect of many-body interactions in real solutions. The results show that the many-body interactions also have a significant impact on the energetic and geometric properties of the CO2 complexes. Moreover, the self-aggregation of strong polar molecules will greatly weaken the effective Lewis acid–base interaction due to the zone overlapping, which needs to be taken into account in the design of future CO2 -philes.

scholarly journals Proteus software for physics-based protein design

2020 ◽  
Author(s):  
David Mignon ◽  
Karen Druart ◽  
Vaitea Opuu ◽  
Savvas Polydorides ◽  
Francesco Villa ◽  
...  
Keyword(s):  
Protein Design ◽  
Catalytic Efficiency ◽  
Trna Synthetase ◽  
Side Chain ◽  
Pdz Domains ◽  
Enzyme Design ◽  
Generalized Born ◽  
Binding Reaction ◽  
Unfolded State ◽  
Replica Exchange Monte Carlo

AbstractWe describe methods and software for physics-based protein design. The folded state energy combines molecular mechanics with Generalized Born solvent. Sequence and conformation space are sampled with Replica Exchange Monte Carlo, assuming one or a few fixed protein backbone structures and discrete side chain rotamers. Whole protein design and enzyme design are presented as illustrations. Full redesign of three PDZ domains was done using a simple, empirical, unfolded state model. Designed sequences were very similar to natural ones. Enzyme redesign exploited a powerful, adaptive, importance sampling approach that allows the design to directly target substrate binding, reaction rate, catalytic efficiency, or the specificity of these properties. Redesign of tyrosyl-tRNA synthetase stereospecificity is reported as an example.

Novel simulation model for many-body multipole dispersion interactions

1998 ◽  
Vol 94 (3) ◽  
pp. 417-433 ◽  
Author(s):  
MARTIN VAN DER HOEF ◽  
PAUL MADDEN
Keyword(s):  
Simulation Model ◽  
Dispersion Interactions ◽  
Many Body

Higher Dietary Acidity is Associated with Lower Bone Mineral Density in Postmenopausal Iranian Women, Independent of Dietary Calcium Intake

2014 ◽  
Vol 84 (3-4) ◽  
pp. 0206-0217 ◽  
Author(s):  
Seyedeh-Elaheh Shariati-Bafghi ◽  
Elaheh Nosrat-Mirshekarlou ◽  
Mohsen Karamati ◽  
Bahram Rashidkhani
Keyword(s):  
Calcium Intake ◽  
Dietary Calcium ◽  
Dietary Calcium Intake ◽  
Dietary Intakes ◽  
Iranian Women ◽  
Acid Base Balance ◽  
Mineral Density ◽  
Acid Base ◽  
Base Balance ◽  
Dietary Acid

Findings of studies on the link between dietary acid-base balance and bone mass are relatively mixed. We examined the association between dietary acid-base balance and bone mineral density (BMD) in a sample of Iranian women, hypothesizing that a higher dietary acidity would be inversely associated with BMD, even when dietary calcium intake is adequate. In this cross-sectional study, lumbar spine and femoral neck BMDs of 151 postmenopausal women aged 50 - 85 years were measured using dual-energy x-ray absorptiometry. Dietary intakes were assessed using a validated food frequency questionnaire. Renal net acid excretion (RNAE), an estimate of acid-base balance, was then calculated indirectly from the diet using the formulae of Remer (based on dietary intakes of protein, phosphorus, potassium, and magnesium; RNAERemer) and Frassetto (based on dietary intakes of protein and potassium; RNAEFrassetto), and was energy adjusted by the residual method. After adjusting for potential confounders, multivariable adjusted means of the lumbar spine BMD of women in the highest tertiles of RNAERemer and RNAEFrassetto were significantly lower than those in the lowest tertiles (for RNAERemer: mean difference -0.084 g/cm2; P=0.007 and for RNAEFrassetto: mean difference - 0.088 g/cm2; P=0.004). Similar results were observed in a subgroup analysis of subjects with dietary calcium intake of >800 mg/day. In conclusion, a higher RNAE (i. e. more dietary acidity), which is associated with greater intake of acid-generating foods and lower intake of alkali-generating foods, may be involved in deteriorating the bone health of postmenopausal Iranian women, even in the context of adequate dietary calcium intake.

Sign in / Sign up

Export Citation Format

Share Document