Thermodynamically effective molecular surfaces for more efficient study of condensed-phase thermodynamics

Author(s):  
Amin Alibakhshi ◽  
bernd hartke

Abstract Evaluation of molecular surfaces plays the key role in a wide range of cutting-edge scientific fields and technologies, due to the well-characterized dependency between molecular surfaces and condensed phase thermodynamics. Numerous methods to evaluate molecular surfaces such as van-der-Waals and solvent accessible surface areas and various parameterizations for each one, have been proposed in the literature and typically yield quite diverse estimations of molecular surfaces. Despite this diversity, numerous successful applications have been reported for each one, which has become possible via ad-hoc modifications and parametrizations employed to accommodate inappropriately defined molecular surfaces. The main aim of the present study is to propose “thermodynamically effective” molecular surface which unlike the conventionally accepted molecular surfaces, can be defined only uniquely, can be measured experimentally for each molecule directly and straightforwardly, is defined based on a well-characterized theoretically described dependency between molecular surfaces and solution thermodynamics, and is highly accurate in evaluating various thermodynamics quantities in solution for a wide temperature range and different types of molecules, without requiring any ad-hoc modification.

1998 ◽  
Vol 3 (4) ◽  
pp. 253-258 ◽  
Author(s):  
Arthur G. Street ◽  
Stephen L. Mayo

2019 ◽  
Vol 35 (18) ◽  
pp. 3499-3501 ◽  
Author(s):  
Judemir Ribeiro ◽  
Carlos Ríos-Vera ◽  
Francisco Melo ◽  
Andreas Schüller

Abstract Summary Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. Availability and implementation A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. Supplementary information Supplementary data are available at Bioinformatics online.


1988 ◽  
Vol 1 (2) ◽  
pp. 103-116 ◽  
Author(s):  
Winnfried Hasel ◽  
Thomas F. Hendrickson ◽  
W.Clark Still

2017 ◽  
Vol 1 (S1) ◽  
pp. 2-2
Author(s):  
Jingran Wen ◽  
Daniel Scoles ◽  
Julio C. Facelli

OBJECTIVES/SPECIFIC AIMS: Polyglutamine (polyQ) neurodegenerative diseases, associated with the unstable expansion of polyQ tracts, are devastating diseases for which no treatments exist. Moreover, most drug discovery attempts have been hindered by the lack of understanding on the relevant pathogenic mechanisms. Here, using previously reported 3D protein predicted structures of ataxin-2 and ataxin-3, we analyze the effect of polyQ enlargement on hydrogen bonding and water accessibility patterns as a possible mechanism for pathogenesis thought enhanced protein aggregation. METHODS/STUDY POPULATION: Using the I-TASSER predicted structures of ataxin-2 and ataxin-3 with different numbers of glutamine repeats representing polyQ lengths characteristic of both normal and pathological tracts (Journal of Biomolecular Structure and Dynamics, 2016: 1–16), we identified hydrogen bonds (HBs, UCSF Chimera FindHBond module) and calculated solvent-accessible surface areas (SASA, DSSP program) for the polyQ tracts available in the 3D structures. RESULTS/ANTICIPATED RESULTS: The identified HBs were analyzed as the function of the number of glutamines in the polyQ tracts and characterized as those intra-polyQ and exter-polyQ, respectively. The SASA of the polyQ region was also studied as the function of the polyQ tract length. DISCUSSION/SIGNIFICANCE OF IMPACT: The results obtained here indicate that polyQ regions increasingly prefer self-interactions, which consistently can lead to more compact polyQ structures. The results strongly support the notion that the expansion of the polyQ region can be an intrinsic force leading to self-aggregation of polyglutamine proteins and suggest that the modulation of solvent-polyQ interactions could be a possible therapeutic strategy for polyQ diseases.


2007 ◽  
Vol 63 (2) ◽  
pp. 270-274 ◽  
Author(s):  
Marian Novotny ◽  
Marvin Seibert ◽  
Gerard J. Kleywegt

All of molecular recognition, from the binding of substrates by enzymes, information transfer in replicating and processing the genetic information to the folding of proteins, is dominated by non-covalent interactions. Perhaps the most difficult challenge is understanding protein folding because each group in the molecule has to recognize with which ones it has to pair. Protein engineering is providing an experimental entry to determine the magnitude, nature and importance of the various levels of recognition in protein folding. In addition to providing the energetics of specific interactions, fundamental information has been given on the energetics of burial of hydrophobic and hydrophilic solvent-accessible surface areas and their specific roles in stabilizing protein cores and helices.


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