401
|
Abstract
The electric polarizability of DNA, represented by the dielectric constant, is a key intrinsic property that modulates DNA interaction with effector proteins. Surprisingly, it has so far remained unknown owing to the lack of experimental tools able to access it. Here, we experimentally resolved it by detecting the ultraweak polarization forces of DNA inside single T7 bacteriophages particles using electrostatic force microscopy. In contrast to the common assumption of low-polarizable behavior like proteins (εr ∼ 2-4), we found that the DNA dielectric constant is ∼ 8, considerably higher than the value of ∼ 3 found for capsid proteins. State-of-the-art molecular dynamic simulations confirm the experimental findings, which result in sensibly decreased DNA interaction free energy than normally predicted by Poisson-Boltzmann methods. Our findings reveal a property at the basis of DNA structure and functions that is needed for realistic theoretical descriptions, and illustrate the synergetic power of scanning probe microscopy and theoretical computation techniques.
Collapse
|
402
|
Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS Comput Biol 2014; 10:e1003748. [PMID: 25101830 PMCID: PMC4125040 DOI: 10.1371/journal.pcbi.1003748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
Collapse
|
403
|
Chao WC, Shen JY, Lu JF, Wang JS, Yang HC, Wee K, Lin LJ, Kuo YC, Yang CH, Weng SH, Huang HC, Chen YH, Chou PT. Probing Water Environment of Trp59 in Ribonuclease T1: Insight of the Structure–Water Network Relationship. J Phys Chem B 2014; 119:2157-67. [DOI: 10.1021/jp503914s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei-Chih Chao
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Jiun-Yi Shen
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | | | | | | | - Kevin Wee
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | | | | | | | | | - Huai-Ching Huang
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - You-Hua Chen
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Pi-Tai Chou
- Department
of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
404
|
Marzinek JK, Bond PJ, Lian G, Zhao Y, Han L, Noro MG, Pistikopoulos EN, Mantalaris A. Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations. J Chem Inf Model 2014; 54:2093-104. [DOI: 10.1021/ci500164q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jan K. Marzinek
- National University of Singapore, Department of Biological
Sciences, 14 Science Drive
4, Singapore 117543
- Bioinformatics
Institute (A*STAR), 30 Biopolis Str.,
#07-01 Matrix, Singapore 138671
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
- Department
of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom
| | - Peter J. Bond
- National University of Singapore, Department of Biological
Sciences, 14 Science Drive
4, Singapore 117543
- Bioinformatics
Institute (A*STAR), 30 Biopolis Str.,
#07-01 Matrix, Singapore 138671
- The
Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Guoping Lian
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, United Kingdom
- Department
of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Yanyan Zhao
- China Agricultural University, Beijing 100083, People’s Republic of China
| | - Lujia Han
- China Agricultural University, Beijing 100083, People’s Republic of China
| | - Massimo G. Noro
- Physical and Chemical Insights Group, Unilever R&D, Port Sunlight, Wirral, CH63 3JW, United Kingdom
| | - Efstratios N. Pistikopoulos
- Department
of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom
| | - Athanasios Mantalaris
- Department
of Chemical Engineering and Chemical Technology, Imperial College London, London, SW7 2BY, United Kingdom
| |
Collapse
|
405
|
Bogár F, Bartha F, Násztor Z, Fábián L, Leitgeb B, Dér A. On the Hofmeister Effect: Fluctuations at the Protein–Water Interface and the Surface Tension. J Phys Chem B 2014; 118:8496-504. [DOI: 10.1021/jp502505c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ferenc Bogár
- MTA-SZTE
Supramolecular and Nanostructured Materials Research Group of Hungarian
Academy of Sciences, University of Szeged, H-6720 Szeged, Hungary
| | - Ferenc Bartha
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
| | - Zoltán Násztor
- Department
of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - László Fábián
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| | - Balázs Leitgeb
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
- Department
of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - András Dér
- Institute
of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, H-6726 Szeged, Hungary
| |
Collapse
|
406
|
Girod M, Enjalbert Q, Brunet C, Antoine R, Lemoine J, Lukac I, Radman M, Krisko A, Dugourd P. Structural basis of protein oxidation resistance: a lysozyme study. PLoS One 2014; 9:e101642. [PMID: 24999730 PMCID: PMC4085010 DOI: 10.1371/journal.pone.0101642] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Accumulation of oxidative damage in proteins correlates with aging since it can cause irreversible and progressive degeneration of almost all cellular functions. Apparently, native protein structures have evolved intrinsic resistance to oxidation since perfectly folded proteins are, by large most robust. Here we explore the structural basis of protein resistance to radiation-induced oxidation using chicken egg white lysozyme in the native and misfolded form. We study the differential resistance to oxidative damage of six different parts of native and misfolded lysozyme by a targeted tandem/mass spectrometry approach of its tryptic fragments. The decay of the amount of each lysozyme fragment with increasing radiation dose is found to be a two steps process, characterized by a double exponential evolution of their amounts: the first one can be largely attributed to oxidation of specific amino acids, while the second one corresponds to further degradation of the protein. By correlating these results to the structural parameters computed from molecular dynamics (MD) simulations, we find the protein parts with increased root-mean-square deviation (RMSD) to be more susceptible to modifications. In addition, involvement of amino acid side-chains in hydrogen bonds has a protective effect against oxidation Increased exposure to solvent of individual amino acid side chains correlates with high susceptibility to oxidative and other modifications like side chain fragmentation. Generally, while none of the structural parameters alone can account for the fate of peptides during radiation, together they provide an insight into the relationship between protein structure and susceptibility to oxidation.
Collapse
Affiliation(s)
- Marion Girod
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Enjalbert
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Brunet
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Iva Lukac
- Mediterranean Institute for Life Sciences, Split, Croatia
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Liverpool, Merseyside, England
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences, Split, Croatia
- INSERM U1001, Faculte de Medecine, Universite R. Descartes Paris-5, Paris, France
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Split, Croatia
- * E-mail: (PD) (AK); (AK) (PD)
| | - Philippe Dugourd
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail: (PD) (AK); (AK) (PD)
| |
Collapse
|
407
|
Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine. Int J Mol Sci 2014; 15:11799-816. [PMID: 24995694 PMCID: PMC4139815 DOI: 10.3390/ijms150711799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 01/26/2023] Open
Abstract
Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized) methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.
Collapse
|
408
|
Kumari R, Kumar R, Lynn A. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 2014; 54:1951-62. [PMID: 24850022 DOI: 10.1021/ci500020m] [Citation(s) in RCA: 2939] [Impact Index Per Article: 293.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks-Chandler-Andersen like integral method). We showcase the effectiveness of the tool by comparing the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes with their experimental binding free energies. The effect of varying several combinations of input parameters such as atomic radii, dielectric constant, grid resolution, solute-solvent dielectric boundary definition, and nonpolar models was investigated. g_mmpbsa can also be used to estimate the energy contribution per residue to the binding energy. It has been used to identify those residues in HIV-1 protease that are most critical for binding a range of inhibitors.
Collapse
Affiliation(s)
- Rashmi Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi 110067, India
| | | | | | | |
Collapse
|
409
|
Heinrich J, Krone M, O'Donoghue SI, Weiskopf D. Visualising intrinsic disorder and conformational variation in protein ensembles. Faraday Discuss 2014; 169:179-93. [PMID: 25340810 DOI: 10.1039/c3fd00138e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered regions (IDRs) in proteins are still not well understood, but are increasingly recognised as important in key biological functions, as well as in diseases. IDRs often confound experimental structure determination-however, they are present in many of the available 3D structures, where they exhibit a wide range of conformations, from ill-defined and highly flexible to well-defined upon binding to partner molecules, or upon post-translational modifications. Analysing such large conformational variations across ensembles of 3D structures can be complex and difficult; our goal in this paper is to improve this situation by augmenting traditional approaches (molecular graphics and principal components) with methods from human-computer interaction and information visualisation, especially parallel coordinates. We present a new tool integrating these approaches, and demonstrate how it can dissect ensembles to reveal functional insights into conformational variation and intrinsic disorder.
Collapse
Affiliation(s)
- Julian Heinrich
- VISUS, University of Stuttgart, Germany. {kroneml
- weiskopf}@visus.uni-stuttgart.de
| | | | | | | |
Collapse
|
410
|
Mondal S, Khelashvili G, Weinstein H. Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins. Biophys J 2014; 106:2305-16. [PMID: 24896109 PMCID: PMC4052241 DOI: 10.1016/j.bpj.2014.04.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/31/2014] [Accepted: 04/23/2014] [Indexed: 01/12/2023] Open
Abstract
The membrane environment, its composition, dynamics, and remodeling, have been shown to participate in the function and organization of a wide variety of transmembrane (TM) proteins, making it necessary to study the molecular mechanisms of such proteins in the context of their membrane settings. We review some recent conceptual advances enabling such studies, and corresponding computational models and tools designed to facilitate the concerted experimental and computational investigation of protein-membrane interactions. To connect productively with the high resolution achieved by cognate experimental approaches, the computational methods must offer quantitative data at an atomistically detailed level. We show how such a quantitative method illuminated the mechanistic importance of a structural characteristic of multihelical TM proteins, that is, the likely presence of adjacent polar and hydrophobic residues at the protein-membrane interface. Such adjacency can preclude the complete alleviation of the well-known hydrophobic mismatch between TM proteins and the surrounding membrane, giving rise to an energy cost of residual hydrophobic mismatch. The energy cost and biophysical formulation of hydrophobic mismatch and residual hydrophobic mismatch are reviewed in the context of their mechanistic role in the function of prototypical members of multihelical TM protein families: 1), LeuT, a bacterial homolog of mammalian neurotransmitter sodium symporters; and 2), rhodopsin and the β1- and β2-adrenergic receptors from the G-protein coupled receptor family. The type of computational analysis provided by these examples is poised to translate the rapidly growing structural data for the many TM protein families that are of great importance to cell function into ever more incisive insights into mechanisms driven by protein-ligand and protein-protein interactions in the membrane environment.
Collapse
Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York.
| |
Collapse
|
411
|
Kreuzer SM, Elber R. Coiled-coil response to mechanical force: global stability and local cracking. Biophys J 2014; 105:951-61. [PMID: 23972847 DOI: 10.1016/j.bpj.2013.05.064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 05/29/2013] [Indexed: 12/01/2022] Open
Abstract
Coiled coils are important structural motifs formed by two or more amphipathic α-helices that twist into a supercoil. These motifs are found in a wide range of proteins, including motor proteins and structural proteins, that are known to transmit mechanical loads. We analyze atomically detailed simulations of coiled-coil cracking under load with Milestoning. Milestoning is an approach that captures the main features of the process in a network, quantifying kinetics and thermodynamics. A 112-residue segment of the β-myosin S2 domain was subjected to constant-magnitude (0-200 pN) and constant-direction tensile forces in molecular dynamics simulations. Twenty 20 ns straightforward simulations at several load levels revealed that initial single-residue cracking events (Ψ > 90°) at loads <100 pN were accompanied by rapid refolding without either intra- or interhelix unfolding propagation. Only initial unfolding events at the highest load (200 pN) regularly propagated along and between helices. Analysis of hydrophobic interactions and of interhelix hydrogen bonds did not show significant variation as a function of load. Unfolding events were overwhelmingly located in the vicinity of E929, a charged residue in a hydrophobic position of the heptad repeat. Milestoning network analysis of E929 cracking determined that the mean first-passage time ranges from 20 ns (200 pN) to 80 ns (50 pN), which is ∼20 times the mean first-passage time of an isolated helix with the same sequence.
Collapse
Affiliation(s)
- Steven M Kreuzer
- Department of Mechanical Engineering, University of Texas, Austin, TX, USA
| | | |
Collapse
|
412
|
Lazutin AA, Glagolev MK, Vasilevskaya VV, Khokhlov AR. Hypercrosslinked polystyrene networks: An atomistic molecular dynamics simulation combined with a mapping/reverse mapping procedure. J Chem Phys 2014; 140:134903. [DOI: 10.1063/1.4869695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
413
|
Scaling behaviour for the water transport in nanoconfined geometries. Nat Commun 2014; 5:4565. [PMID: 24699509 PMCID: PMC3988813 DOI: 10.1038/ncomms4565] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/05/2014] [Indexed: 12/16/2022] Open
Abstract
The transport of water in nanoconfined geometries is different from bulk phase and has tremendous implications in nanotechnology and biotechnology. Here molecular dynamics is used to compute the self-diffusion coefficient D of water within nanopores, around nanoparticles, carbon nanotubes and proteins. For almost 60 different cases, D is found to scale linearly with the sole parameter θ as D(θ)=DB[1+(DC/DB−1)θ], with DB and DC the bulk and totally confined diffusion of water, respectively. The parameter θ is primarily influenced by geometry and represents the ratio between the confined and total water volumes. The D(θ) relationship is interpreted within the thermodynamics of supercooled water. As an example, such relationship is shown to accurately predict the relaxometric response of contrast agents for magnetic resonance imaging. The D(θ) relationship can help in interpreting the transport of water molecules under nanoconfined conditions and tailoring nanostructures with precise modulation of water mobility. A precise control of water transport in different configurations is crucial for many technological applications. Chiavazzo et al. define a dimensionless scaling parameter to fully describe the water self-diffusion coefficient in various nanoconfined geometries using molecular dynamic simulations.
Collapse
|
414
|
Hayes RL, Noel JK, Whitford PC, Mohanty U, Sanbonmatsu KY, Onuchic JN. Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophys J 2014; 106:1508-19. [PMID: 24703312 PMCID: PMC3976530 DOI: 10.1016/j.bpj.2014.01.042] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/22/2014] [Accepted: 01/29/2014] [Indexed: 12/17/2022] Open
Abstract
The stability of RNA tertiary structures depends heavily on Mg(2+). The Mg(2+)-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg(2+) associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg(2+) ions interact closely and strongly with the RNA, unlike monovalent ions such as K(+), suggesting that an explicit treatment of Mg(2+) is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg(2+)-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg(2+) through the explicit representation of Mg(2+) ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K(+) and models its competition with condensed Mg(2+). The model contains one fitted parameter, the number of condensed K(+) ions in the absence of Mg(2+). Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ2+ to the Mg(2+)-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg(2+) and RNA dynamics.
Collapse
Affiliation(s)
- Ryan L Hayes
- Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas
| | - Jeffrey K Noel
- Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Udayan Mohanty
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Labs, Los Alamos, New Mexico.
| | - José N Onuchic
- Center for Theoretical Biological Physics and Department of Physics and Astronomy, Rice University, Houston, Texas; Department of Chemistry and Department of Biochemistry and Cell Biology, Rice University, Houston, Texas.
| |
Collapse
|
415
|
Côté S, Wei G, Mousseau N. Atomistic mechanisms of huntingtin N-terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations. Proteins 2014; 82:1409-27. [PMID: 24415136 DOI: 10.1002/prot.24509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/27/2013] [Accepted: 01/06/2014] [Indexed: 01/14/2023]
Abstract
The huntingtin protein is characterized by a segment of consecutive glutamines (Q(N)) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N-terminal 17-amino-acid sequence (htt(NT)) positioned just before the Q(N) region is important for the binding of huntingtin to membranes. Through all-atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt(NT)Q(N) fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps-approach, reorganization, anchoring, and insertion-that are very diverse at the atomic level. On the membrane, the htt(NT) peptide forms a stable α-helix essentially parallel to the membrane with its nonpolar side-chains-mainly Leu-4, Leu-7, Phe-11 and Leu-14-positioned in the hydrophobic core of the membrane. Salt-bridges involving Glu-5, Glu-12, Lys-6, and Lys-15, as well as hydrogen bonds involving Thr-3 and Ser-13 with the phospholipids also stabilize the structure and orientation of the htt(NT) peptide. These observations do not significantly change upon adding the Q(N) region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt(NT) region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q(N) region could also play a key role for the oligomerization of htt(NT)Q(N) on phospholipid membranes.
Collapse
Affiliation(s)
- Sébastien Côté
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, Montréal (Québec), Canada
| | | | | |
Collapse
|
416
|
Ghosh A, Sonavane U, Joshi R. Multiscale modelling to understand the self-assembly mechanism of human β2-adrenergic receptor in lipid bilayer. Comput Biol Chem 2014; 48:29-39. [DOI: 10.1016/j.compbiolchem.2013.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/06/2013] [Accepted: 11/07/2013] [Indexed: 11/27/2022]
|
417
|
Sun L, Li X, Hede T, Tu Y, Leck C, Ågren H. Molecular dynamics simulations reveal the assembly mechanism of polysaccharides in marine aerosols. Phys Chem Chem Phys 2014; 16:25935-41. [DOI: 10.1039/c4cp03423f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This figure represents the configuration of the marine gel after the polysaccharides undergo self-assembly. The calcium cations are blended inside the assembly and they act as ionic bridges.
Collapse
Affiliation(s)
- Lu Sun
- Department of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology
- S-10691 Stockholm, Sweden
| | - Xin Li
- Department of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology
- S-10691 Stockholm, Sweden
| | - Thomas Hede
- Department of Meteorology
- Stockholm University
- S-10691 Stockholm, Sweden
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology
- S-10691 Stockholm, Sweden
| | - Caroline Leck
- Department of Meteorology
- Stockholm University
- S-10691 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology
- S-10691 Stockholm, Sweden
| |
Collapse
|
418
|
Cino EA, Choy WY, Karttunen M. Conformational Biases of Linear Motifs. J Phys Chem B 2013; 117:15943-57. [DOI: 10.1021/jp407536p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elio A. Cino
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Wing-Yiu Choy
- Department
of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
| | - Mikko Karttunen
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
419
|
Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS One 2013; 8:e79482. [PMID: 24244510 PMCID: PMC3828330 DOI: 10.1371/journal.pone.0079482] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/22/2013] [Indexed: 11/30/2022] Open
Abstract
Phenylalanine hydroxylase (PAH) catalyzes the conversion of L-Phe to L-Tyr. Defects in PAH activity, caused by mutations in the human gene, result in the autosomal recessively inherited disease hyperphenylalaninemia. PAH activity is regulated by multiple factors, including phosphorylation and ligand binding. In particular, PAH displays positive cooperativity for L-Phe, which is proposed to bind the enzyme on an allosteric site in the N-terminal regulatory domain (RD), also classified as an ACT domain. This domain is found in several proteins and is able to bind amino acids. We used molecular dynamics simulations to obtain dynamical and structural insights into the isolated RD of PAH. Here we show that the principal motions involve conformational changes leading from an initial open to a final closed domain structure. The global intrinsic motions of the RD are correlated with exposure to solvent of a hydrophobic surface, which corresponds to the ligand binding-site of the ACT domain. Our results strongly suggest a relationship between the Phe-binding function and the overall dynamic behaviour of the enzyme. This relationship may be affected by structure-disturbing mutations. To elucidate the functional implications of the mutations, we investigated the structural effects on the dynamics of the human RD PAH induced by six missense hyperphenylalaninemia-causing mutations, namely p.G46S, p.F39C, p.F39L, p.I65S, p.I65T and p.I65V. These studies showed that the alterations in RD hydrophobic interactions induced by missense mutations could affect the functionality of the whole enzyme.
Collapse
|
420
|
Abstract
Spatial organization of G-protein coupled receptors (GPCRs) into dimers and higher order oligomers has been demonstrated in vitro and in vivo. The pharmacological readout was shown to depend on the specific interfaces, but why particular regions of the GPCR structure are involved, and how ligand-determined states change them remains unknown. Here we show why protein-membrane hydrophobic matching is attained upon oligomerization at specific interfaces from an analysis of coarse-grained molecular dynamics simulations of the spontaneous diffusion-interaction of the prototypical beta2-adrenergic (β2AR) receptors in a POPC lipid bilayer. The energy penalty from mismatch is significantly reduced in the spontaneously emerging oligomeric arrays, making the spatial organization of the GPCRs dependent on the pattern of mismatch in the monomer. This mismatch pattern is very different for β2AR compared to the highly homologous and structurally similar β1AR, consonant with experimentally observed oligomerization patterns of β2AR and β1AR. The results provide a mechanistic understanding of the structural context of oligomerization.
Collapse
|
421
|
Smiatek J, Harishchandra RK, Galla HJ, Heuer A. Low concentrated hydroxyectoine solutions in presence of DPPC lipid bilayers: A computer simulation study. Biophys Chem 2013; 180-181:102-9. [DOI: 10.1016/j.bpc.2013.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/05/2013] [Accepted: 07/05/2013] [Indexed: 02/05/2023]
|
422
|
Storm S, Jakobtorweihen S, Smirnova I, Panagiotopoulos AZ. Molecular dynamics simulation of SDS and CTAB micellization and prediction of partition equilibria with COSMOmic. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11582-92. [PMID: 23941607 DOI: 10.1021/la402415b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular dynamics (MD) simulations of the self-assembly of different ionic surfactants have been performed in order to obtain representative micellar structures. Subsequently, these structures were used to predict the partition behavior of various solutes in these micelles with COSMOmic, an extension of COSMO-RS. This paper includes multiple self-assembled micelles of SDS (sodium dodecyl sulfate, anionic surfactant) and CTAB (cetyltrimethylammoniumbromide, cationic surfactant) at different concentrations. Micellar size, density profiles, and shape (eccentricity) have been investigated. However, the size strongly depends on the functional definition of a micelle. For this reason, we present a method based on the free monomer concentration in aqueous solution as an optimization criterion for the micelle definition. The combination of MD with COSMOmic has the benefit of combining detailed atomistic information from MD with fast calculations of COSMOmic. For the first time the influence of micelle structure on pratition equilibria, predicted with COSMOmic, were investigated. In case of SDS more than 4600 and for CTAB more than 800 single micelles have been studied. The predictions of the partition coefficients with COSMOmic are in good agreement with experimental data. Additionally, the most favorable locations of selected molecules in the micelles as well as probable energy barriers are determined even for complex solutes such as toluene, propanolol, ephedrine, acetone, phenol, lidocaine, syringic acid, coumarin, isovanillin, ferulic acid, and vanillic acid. This method can therefore be applied as a potential screening tool for solutes (e.g., drugs) to find the optimal solute-surfactant combination.
Collapse
Affiliation(s)
- Sandra Storm
- Institute of Thermal Separation Processes, ‡Institute of Chemical Reaction Engineering, Hamburg University of Technology , D-21073 Hamburg, Germany
| | | | | | | |
Collapse
|
423
|
Marzinek JK, Lian G, Marzinek JK, Mantalaris A, Pistikopoulos EN, Zhao Y, Han L, Chen L, Bond PJ, Noro MG. Molecular and thermodynamic basis for EGCG-Keratin interaction-part I: Molecular dynamics simulations. AIChE J 2013. [DOI: 10.1002/aic.14220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jan K. Marzinek
- Unilever Discover, Unilever R&D, Colworth, Sharnbrook; Bedfordshire MK44 1LQ U.K
| | - Guoping Lian
- Unilever Discover, Unilever R&D, Colworth, Sharnbrook; Bedfordshire MK44 1LQ U.K
| | - Jan K. Marzinek
- Dept. of Chemical Engineering, Centre for Process Systems Engineering (CPSE); Imperial College London; London SW7 2BY U.K
| | - Athanasios Mantalaris
- Dept. of Chemical Engineering, Centre for Process Systems Engineering (CPSE); Imperial College London; London SW7 2BY U.K
| | - Efstratios N. Pistikopoulos
- Dept. of Chemical Engineering, Centre for Process Systems Engineering (CPSE); Imperial College London; London SW7 2BY U.K
| | - Yanyan Zhao
- College of Engineering; China Agricultural University; Beijing 100083 P. R. China
| | - Lujia Han
- College of Engineering; China Agricultural University; Beijing 100083 P. R. China
| | - Longjian Chen
- College of Engineering; China Agricultural University; Beijing 100083 P. R. China
| | - Peter J. Bond
- Dept. of Chemistry, The Unilever Centre for Molecular Science Informatics; University of Cambridge; Lensfield Road Cambridge CB2 1EW U.K
| | - Massimo G. Noro
- Physical and Chemical Insights Group, Unilever R&D, Port Sunlight; Wirral CH63 3JW U.K
| |
Collapse
|
424
|
Peng Z, Oldfield CJ, Xue B, Mizianty MJ, Dunker AK, Kurgan L, Uversky VN. A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome. Cell Mol Life Sci 2013; 71:1477-504. [PMID: 23942625 PMCID: PMC7079807 DOI: 10.1007/s00018-013-1446-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 01/01/2023]
Abstract
Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.
Collapse
Affiliation(s)
- Zhenling Peng
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | | | | | | | | | | | | |
Collapse
|
425
|
Fluorescence quenching of the phycobilisome terminal emitter LCM from the cyanobacterium Synechocystis sp. PCC 6803 detected in vivo and in vitro. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 125:137-45. [DOI: 10.1016/j.jphotobiol.2013.05.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/30/2013] [Accepted: 05/30/2013] [Indexed: 11/21/2022]
|
426
|
Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013; 425:3338-59. [PMID: 23811057 DOI: 10.1016/j.jmb.2013.06.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/15/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022]
Abstract
Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of Aβ aggregation pathways.
Collapse
Affiliation(s)
- David J Rosenman
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | | | | | | | | |
Collapse
|
427
|
Huang X, Han K, Zhu Y. Systematic optimization model and algorithm for binding sequence selection in computational enzyme design. Protein Sci 2013; 22:929-41. [PMID: 23649589 DOI: 10.1002/pro.2275] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 03/14/2013] [Accepted: 04/27/2013] [Indexed: 01/04/2023]
Abstract
A systematic optimization model for binding sequence selection in computational enzyme design was developed based on the transition state theory of enzyme catalysis and graph-theoretical modeling. The saddle point on the free energy surface of the reaction system was represented by catalytic geometrical constraints, and the binding energy between the active site and transition state was minimized to reduce the activation energy barrier. The resulting hyperscale combinatorial optimization problem was tackled using a novel heuristic global optimization algorithm, which was inspired and tested by the protein core sequence selection problem. The sequence recapitulation tests on native active sites for two enzyme catalyzed hydrolytic reactions were applied to evaluate the predictive power of the design methodology. The results of the calculation show that most of the native binding sites can be successfully identified if the catalytic geometrical constraints and the structural motifs of the substrate are taken into account. Reliably predicting active site sequences may have significant implications for the creation of novel enzymes that are capable of catalyzing targeted chemical reactions.
Collapse
Affiliation(s)
- Xiaoqiang Huang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | | | | |
Collapse
|
428
|
Erbaş A, Netz RR. Confinement-dependent friction in peptide bundles. Biophys J 2013; 104:1285-95. [PMID: 23528088 PMCID: PMC3602766 DOI: 10.1016/j.bpj.2013.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/06/2012] [Accepted: 02/07/2013] [Indexed: 11/17/2022] Open
Abstract
Friction within globular proteins or between adhering macromolecules crucially determines the kinetics of protein folding, the formation, and the relaxation of self-assembled molecular systems. One fundamental question is how these friction effects depend on the local environment and in particular on the presence of water. In this model study, we use fully atomistic MD simulations with explicit water to obtain friction forces as a single polyglycine peptide chain is pulled out of a bundle of k adhering parallel polyglycine peptide chains. The whole system is periodically replicated along the peptide axes, so a stationary state at prescribed mean sliding velocity V is achieved. The aggregation number is varied between k = 2 (two peptide chains adhering to each other with plenty of water present at the adhesion sites) and k = 7 (one peptide chain pulled out from a close-packed cylindrical array of six neighboring peptide chains with no water inside the bundle). The friction coefficient per hydrogen bond, extrapolated to the viscous limit of vanishing pulling velocity V → 0, exhibits an increase by five orders of magnitude when going from k = 2 to k = 7. This dramatic confinement-induced friction enhancement we argue to be due to a combination of water depletion and increased hydrogen-bond cooperativity.
Collapse
Affiliation(s)
- Aykut Erbaş
- Free University of Berlin, Fachbereich Physik, Berlin, Germany.
| | | |
Collapse
|
429
|
Nicolau DV, Paszek E, Fulga F, Nicolau DV. Protein molecular surface mapped at different geometrical resolutions. PLoS One 2013; 8:e58896. [PMID: 23516572 PMCID: PMC3597524 DOI: 10.1371/journal.pone.0058896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 02/08/2013] [Indexed: 01/08/2023] Open
Abstract
Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.
Collapse
Affiliation(s)
- Dan V Nicolau
- Department of Electrical Engineering & Electronics, University of Liverpool, Liverpool, United Kingdom.
| | | | | | | |
Collapse
|
430
|
Jakobtorweihen S, Ingram T, Smirnova I. Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane-water partition coefficients. J Comput Chem 2013; 34:1332-40. [DOI: 10.1002/jcc.23262] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 12/28/2022]
|
431
|
Leay L, Siperstein FR. Single Polymer Chain Surface Area as a Descriptor for Rapid Screening of Microporous Polymers for Gas Adsorption. ADSORPT SCI TECHNOL 2013. [DOI: 10.1260/0263-6174.31.1.99] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Laura Leay
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Flor R. Siperstein
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| |
Collapse
|
432
|
Xue B, Brown CJ, Dunker AK, Uversky VN. Intrinsically disordered regions of p53 family are highly diversified in evolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:725-38. [PMID: 23352836 DOI: 10.1016/j.bbapap.2013.01.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 12/28/2012] [Accepted: 01/11/2013] [Indexed: 11/15/2022]
Abstract
Proteins of the p53 family are expressed in vertebrates and in some invertebrate species. The main function of these proteins is to control and regulate cell cycle in response to various cellular signals, and therefore to control the organism's development. The regulatory functions of the p53 family members originate mostly from their highly-conserved and well-structured DNA-binding domains. Many human diseases (including various types of cancer) are related to the missense mutations within this domain. The ordered DNA-binding domains of the p53 family members are surrounded by functionally important intrinsically disordered regions. In this study, substitution rates and propensities in different regions of p53 were analyzed. The analyses revealed that the ordered DNA-binding domain is conserved, whereas disordered regions are characterized by high sequence diversity. This diversity was reflected both in the number of substitutions and in the types of substitutions to which each amino acid was prone. These results support the existence of a positive correlation between protein intrinsic disorder and sequence divergence during the evolutionary process. This higher sequence divergence provides strong support for the existence of disordered regions in p53 in vivo for if they were structured, they would evolve at similar rates as the rest of the protein.
Collapse
Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | | | | |
Collapse
|
433
|
Abstract
Distortions in the DNA sequence such as damages or mispairs are specifically recognized and processed by DNA repair enzymes. A particular challenge for the enzymatic specificity is the recognition of a wrongly-placed native nucleotide such as thymine in T:G mispairs. An important step of substrate binding which is observed in many repair proteins is the flipping of the target base out of the DNA helix into the enzyme's active site. In this work we investigate how much the intrinsic dynamics of mispaired DNA is changed compared to canonical DNA. Our molecular dynamics simulations of DNA with and without T:G mispairs show significant differences in the conformation of paired and mispaired DNA. The wobble pair T:G shows local distortions such as twist, shear and stretch which deviate from canonical B form values. Moreover, the T:G mispair is found to be kinetically less stable, exhibiting two states with respect to base opening: a closed state comparable to the canonical base pairs, and a more open state, indicating a proneness for base flip. In addition, we observe that the thymine base in a T:G mispair is significantly more probable to be flipped than thymine in a T:A pair or cytosine in a C:G pair. Such local deformations and in particular the existence of a second, more-open state can be speculated to help the target-site recognition by repair enzymes.
Collapse
|
434
|
Fressancourt-Collinet M, Hong B, Leclercq L, Alsters PL, Aubry JM, Nardello-Rataj V. Acidic Three-Liquid-Phase Microemulsion Systems Based on Balanced Catalytic Surfactant for Epoxidation and Sulfide Oxidation under Mild Conditions. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201200514] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
435
|
Huang X, Yang J, Zhu Y. A solvated ligand rotamer approach and its application in computational protein design. J Mol Model 2012. [PMID: 23192355 DOI: 10.1007/s00894-012-1695-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The structure-based design of protein-ligand interfaces with respect to different small molecules is of great significance in the discovery of functional proteins. By statistical analysis of a set of protein-ligand complex structures, it was determined that water-mediated hydrogen bonding at the protein-ligand interface plays a crucial role in governing the binding between the protein and the ligand. Based on the novel statistic results, a solvated ligand rotamer approach was developed to explicitly describe the key water molecules at the protein-ligand interface and a water-mediated hydrogen bonding model was applied in the computational protein design context to complement the continuum solvent model. The solvated ligand rotamer approach produces only one additional solvated rotamer for each rotamer in the ligand rotamer library and does not change the number of side-chain rotamers at each protein design site. This has greatly reduced the total combinatorial number in sequence selection for protein design, and the accuracy of the model was confirmed by two tests. For the water placement test, 61% of the crystal water molecules were predicted correctly in five protein-ligand complex structures. For the sequence recapitulation test, 44.7% of the amino acid identities were recovered using the solvated ligand rotamer approach and the water-mediated hydrogen bonding model, while only 30.4% were recovered when the explicitly bound waters were removed. These results indicated that the developed solvated ligand rotamer approach is promising for functional protein design targeting novel protein-ligand interactions.
Collapse
Affiliation(s)
- Xiaoqiang Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | | | | |
Collapse
|
436
|
Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach. J Biol Inorg Chem 2012; 17:543-55. [PMID: 22286956 DOI: 10.1007/s00775-012-0875-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
Abstract
Hydrogenases are metalloenzymes that catalyze the reversible reaction H(2)<->2H(+) + 2e(-), being potentially useful in H(2) production or oxidation. [NiFeSe] hydrogenases are a particularly interesting subgroup of the [NiFe] class that exhibit tolerance to O(2) inhibition and produce more H(2) than standard [NiFe] hydrogenases. However, the molecular determinants responsible for these properties remain unknown. Hydrophobic pathways for H(2) diffusion have been identified in [NiFe] hydrogenases, as have proton transfer pathways, but they have never been studied in [NiFeSe] hydrogenases. Our aim was, for the first time, to characterize the H(2) and proton pathways in a [NiFeSe] hydrogenase and compare them with those in a standard [NiFe] hydrogenase. We performed molecular dynamics simulations of H(2) diffusion in the [NiFeSe] hydrogenase from Desulfomicrobium baculatum and extended previous simulations of the [NiFe] hydrogenase from Desulfovibrio gigas (Teixeira et al. in Biophys J 91:2035-2045, 2006). The comparison showed that H(2) density near the active site is much higher in [NiFeSe] hydrogenase, which appears to have an alternative route for the access of H(2) to the active site. We have also determined a possible proton transfer pathway in the [NiFeSe] hydrogenase from D. baculatum using continuum electrostatics and Monte Carlo simulation and compared it with the proton pathway we found in the [NiFe] hydrogenase from D. gigas (Teixeira et al. in Proteins 70:1010-1022, 2008). The residues constituting both proton transfer pathways are considerably different, although in the same region of the protein. These results support the hypothesis that some of the special properties of [NiFeSe] hydrogenases could be related to differences in the H(2) and proton pathways.
Collapse
|
437
|
Hung SW, Hsiao PY, Lu MC, Chieng CC. Thermodynamic Investigations Using Molecular Dynamics Simulations with Potential of Mean Force Calculations for Cardiotoxin Protein Adsorption on Mixed Self-Assembled Monolayers. J Phys Chem B 2012; 116:12661-8. [DOI: 10.1021/jp304695w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Shih-Wei Hung
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Pai-Yi Hsiao
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Chang Lu
- Department
of Mechanical Engineering, National Chiao Tung University, Hsinchu, Taiwan
| | - Ching-Chang Chieng
- Department of Engineering
and
System Science, National Tsing Hua University, Hsinchu, Taiwan
- Department
of Mechanical and Biomedical
Engineering, City University of Hong Kong, Kowloon, Hong Kong
| |
Collapse
|
438
|
Côté S, Wei G, Mousseau N. All-Atom Stability and Oligomerization Simulations of Polyglutamine Nanotubes with and without the 17-Amino-Acid N-Terminal Fragment of the Huntingtin Protein. J Phys Chem B 2012; 116:12168-79. [DOI: 10.1021/jp306661c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sébastien Côté
- Département de Physique
and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale
Centre-ville, Montréal (Québec), Canada
| | - Guanghong Wei
- State Key Laboratory of Surface
Physics and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, China
| | - Normand Mousseau
- Département de Physique
and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale
Centre-ville, Montréal (Québec), Canada
| |
Collapse
|
439
|
Abel S, Dupradeau FY, Marchi M. Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water. J Chem Theory Comput 2012; 8:4610-23. [DOI: 10.1021/ct3003207] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stéphane Abel
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
| | - François-Yves Dupradeau
- Laboratoire des glucides, UFR de Pharmacie & CNRS FRE 3517, Université de Picardie-Jules Verne, Amiens, France
| | - Massimo Marchi
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
| |
Collapse
|
440
|
Ellis CR, Maiti B, Noid WG. Specific and nonspecific effects of glycosylation. J Am Chem Soc 2012; 134:8184-93. [PMID: 22524526 DOI: 10.1021/ja301005f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosylation regulates vital cellular processes and dramatically influences protein folding and stability. In particular, experiments have demonstrated that asparagine (N)-linked disaccharides drive a "conformational switch" in a model peptide. The present work investigates this conformational switch via extensive atomically detailed replica exchange molecular dynamics simulations in explicit solvent. To distinguish the effects of specific and nonspecific interactions upon the peptide conformational ensemble, these simulations considered model peptides that were N-linked to a disaccharide and to a steric crowder of the same shape. The simulations are remarkably consistent with experiment and provide detailed insight into the peptide structure ensemble. They suggest that steric crowding by N-linked disaccharides excludes extended conformations, but does not significantly impact the tetrahedral structure of the surrounding solvent or otherwise alter the peptide free energy surface. However, the combination of steric crowding with specific hydrogen bonds and hydrophobic stacking interactions more dramatically impacts the peptide ensemble and stabilizes new structures.
Collapse
Affiliation(s)
- Christopher R Ellis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | | | | |
Collapse
|
441
|
Côté S, Laghaei R, Derreumaux P, Mousseau N. Distinct dimerization for various alloforms of the amyloid-beta protein: Aβ(1-40), Aβ(1-42), and Aβ(1-40)(D23N). J Phys Chem B 2012; 116:4043-55. [PMID: 22409719 DOI: 10.1021/jp2126366] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Amyloid-beta protein is related to Alzheimer's disease, and various experiments have shown that oligomers as small as the dimer are cytotoxic. Two alloforms are mainly produced: Aβ(1-40) and Aβ(1-42). They have very different oligomer distributions, and it was recently suggested, from experimental studies, that this variation may originate from structural differences in their dimer structures. Little structural information is available on the Aβ dimer, however, and to complement experimental observations, we simulated the folding of the wild-type Aβ(1-40) and Aβ(1-42) dimers as well as the mutated Aβ(1-40)(D23N) dimer using an accurate coarse-grained force field coupled to Hamiltonian-temperature replica exchange molecular dynamics. The D23N variant impedes the salt-bridge formation between D23 and K28 seen in the wild-type Aβ, leading to very different fibrillation properties and final amyloid fibrils. Our results show that the Aβ(1-42) dimer has a higher propensity than the Aβ(1-40) dimer to form β-strands at the central hydrophobic core (residues 17-21) and at the C-terminal (residues 30-42), which are two segments crucial to the oligomerization of Aβ. The free energy landscape of the Aβ(1-42) dimer is also broader and more complex than that of the Aβ(1-40) dimer. Interestingly, D23N also impacts the free energy landscape by increasing the population of configurations with higher β-strand propensities when compared against Aβ(40). In addition, while Aβ(1-40)(D23N) displays a higher β-strand propensity at the C-terminal, its solvent accessibility does not change with respect to the wild-type sequence. Overall, our results show the strong impact of the two amino acids Ile41-Ala42 and the salt-bridge D23-K28 on the folding of the Aβ dimer.
Collapse
Affiliation(s)
- Sébastien Côté
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, Montréal, Québec, Canada
| | | | | | | |
Collapse
|
442
|
Kim DS, Ryu J, Shin H, Cho Y. Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets. J Comput Chem 2012; 33:1252-73. [PMID: 22396194 DOI: 10.1002/jcc.22956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 12/24/2011] [Accepted: 01/28/2012] [Indexed: 11/11/2022]
Abstract
Given a set of spherical balls, called atoms, in three-dimensional space, its mass properties such as the volume and the boundary area of the union of the atoms are important for many disciplines, particularly for computational chemistry/biology and structural molecular biology. Despite many previous studies, this seemingly easy problem of computing mass properties has not been well-solved. If the mass properties of the union of the offset of the atoms are to be computed as well, the problem gets even harder. In this article, we propose algorithms that compute the mass properties of both the union of atoms and their offsets both correctly and efficiently. The proposed algorithms employ an approach, called the Beta-decomposition, based on the recent theory of the beta-complex. Given the beta-complex of an atom set, these algorithms decompose the target mass property into a set of primitives using the simplexes of the beta-complex. Then, the molecular mass property is computed by appropriately summing up the mass property corresponding to each simplex. The time complexity of the proposed algorithm is O(m) in the worst case where m is the number of simplexes in the beta-complex that can be efficiently computed from the Voronoi diagram of the atoms. It is known in ℝ(3) that m = O(n) on average for biomolecules and m = O(n(2)) in the worst case for general spheres where n is the number of atoms. The theory is first introduced in ℝ(2) and extended to ℝ(3). The proposed algorithms were implemented into the software BetaMass and thoroughly tested using molecular structures available in the Protein Data Bank. BetaMass is freely available at the Voronoi Diagram Research Center web site.
Collapse
Affiliation(s)
- Deok-Soo Kim
- Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea.
| | | | | | | |
Collapse
|
443
|
Pandey YN, Doxastakis M. Detailed atomistic Monte Carlo simulations of a polymer melt on a solid surface and around a nanoparticle. J Chem Phys 2012; 136:094901. [DOI: 10.1063/1.3689316] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
444
|
Palermo NY, Thomas P, Murphy RF, Lovas S. Hexapeptide fragment of carcinoembryonic antigen which acts as an agonist of heterogeneous ribonucleoprotein M. J Pept Sci 2012; 18:252-60. [PMID: 22392880 DOI: 10.1002/psc.2393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 12/08/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022]
Abstract
Colorectal cancers with metastatic potential secrete the glycoprotein carcinoembryonic antigen (CEA). CEA has been implicated in colorectal cancer metastasis by inducing Kupffer cells to produce inflammatory cytokines which, in turn, make the hepatic micro-environment ideal for tumor cell implantation. CEA binds to the heterogeneous ribonucleoprotein M (hnRNP M) which acts as a cell surface receptor in Kupffer cells. The amino acid sequence in CEA, which binds the hnRNP M receptor, is Tyr-Pro-Glu-Leu-Pro-Lys. In this study, the structure of Ac-Tyr-Pro-Glu-Leu-Pro-Lys-NH₂ (YPELPK) was investigated using electronic circular dichroism, vibrational circular dichroism, and molecular dynamics simulations. The binding of the peptide to hnRNP M was also investigated using molecular docking calculations. The biological activity of YPELPK was studied using differentiated human THP-1 cells, which express hnRNP M on their surface and secrete IL-6 when stimulated by CEA. YPELPK forms a stable polyproline-II helix and stimulates IL-6 production of THP-1 cells at micromolar concentrations.
Collapse
Affiliation(s)
- Nicholas Y Palermo
- Departments of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
| | | | | | | |
Collapse
|
445
|
Zhang C, Lai L. Automatch: Target-binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds. Proteins 2012; 80:1078-94. [DOI: 10.1002/prot.24009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 11/10/2022]
|
446
|
Cai Q, Ye X, Wang J, Luo R. On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods. J Chem Theory Comput 2011; 7:3608-3619. [PMID: 24772042 PMCID: PMC3998210 DOI: 10.1021/ct200389p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.
Collapse
Affiliation(s)
- Qin Cai
- Department of Biomedical Engineering, University of California, Irvine, California
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
| | - Xiang Ye
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
- Department of Physics, Shanghai Normal University, Shanghai, China
| | - Jun Wang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
| | - Ray Luo
- Department of Biomedical Engineering, University of California, Irvine, California
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
| |
Collapse
|
447
|
Smiatek J, Chen C, Liu D, Heuer A. Stable conformations of a single stranded deprotonated DNA i-motif. J Phys Chem B 2011; 115:13788-95. [PMID: 21995652 DOI: 10.1021/jp208640a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present molecular dynamics simulations of a single stranded deprotonated DNA i-motif in explicit solvent. Our results indicate that hairpin structures are stable equilibrium conformations at 300 K. The entropic preference of these configurations is explained by strong water ordering effects due to the present number of hydrogen bonds. We observe a full unfolding at higher temperatures in good agreement with experimental results.
Collapse
Affiliation(s)
- Jens Smiatek
- Institut für Physikalische Chemie, Universität Münster, D-48149 Münster, Germany.
| | | | | | | |
Collapse
|
448
|
Comparison of the structural basis for thermal stability between archaeal and bacterial proteins. Extremophiles 2011; 16:67-78. [PMID: 22015540 DOI: 10.1007/s00792-011-0406-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
In this study, the structural basis for thermal stability in archaeal and bacterial proteins was investigated. There were many common factors that confer resistance to high temperature in both archaeal and bacterial proteins. These factors include increases in the Lys content, the bends and blanks of secondary structure, the Glu content of salt bridge; decreases in the number of main-side chain hydrogen bond and exposed surface area, and changes in the bends and blanks of amino acids. Certainly, the utilization of charged amino acids to form salt bridges is a primary factor. In both heat-resistant archaeal and bacterial proteins, most Glu and Asp participate in the formation of salt bridges. Other factors may influence either archaeal or bacterial protein thermostability, which includes the more frequent occurrence of shorter 3(10)-helices and increased hydrophobicity in heat-resistant archaeal proteins. However, there were increases in average helix length, the Glu content in salt bridges, temperature factors and decreases in the number of main-side chain hydrogen bonds, uncharged-uncharged hydrogen bonds, hydrophobicity, and buried and exposed polar surface area in heat-resistant bacterial proteins. Evidently, there are few similarities and many disparities between the heat-resistant mechanisms of archaeal and bacterial proteins.
Collapse
|
449
|
Chunsrivirot S, Santiso E, Trout BL. Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 2: preferential binding to local sites on a surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12396-12404. [PMID: 21936549 DOI: 10.1021/la202593u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Crystallization, a separation and purification process, is commonly used to produce a wide range of materials in various industries, and it usually begins with heterogeneous nucleation on a foreign surface in industrial practice and most other circumstances. Recent studies show that amorphous polymeric substrates are useful in controlling crystallization and selectively producing pharmaceutical polymorphs. In our previous publication, we investigated the possible correlation of the binding affinity of one molecule to key binding sites (local binding), and the possibility of using this binding affinity to guide the selection of polymers promoting heterogeneous nucleation. The studied systems were aspirin binding to four nonporous cross-linked polymers in ethanol-water 38 v% mixture. Cross-linked with divinylbenzene (DVB), these polymers were poly(4-acryloylmorpholine) (PAM), poly(2-carboxyethyl acrylate) (PCEA), poly(4-hydroxylbutyl acrylate) (PHBA), and polystyrene (PS). We discovered that the trend of the magnitudes of the average free energies of binding to the best sites is very similar to that of heterogeneous nucleation activities. This Article aims to investigate whether or not local binding to key sites is the important variable to describe heterogeneous nucleation as opposed to the overall/average binding affinity of molecules to a surface, and to investigate the possibility of using the overall binding affinity to guide the selection of polymers. We used the polymer surfaces generated from our previous study to calculate the overall binding affinity of aspirin molecules to the surface as measured by the preferential interaction coefficients of aspirin (1 m) to these polymers. We discovered that the trend of the average preferential interaction coefficients does not correlate as well to that of heterogeneous nucleation activities as the free energies of binding to the best sites. We also computed the average numbers of aspirin molecules associated with the areas of the surfaces' best binding sites and found that they correlate better to heterogeneous nucleation activities than the average preferential interaction coefficients. These results further support that local binding is indicative of heterogeneous nucleation. Moreover, we found a weak trend of the distance order parameters of the aspirin molecules to be similar that of heterogeneous nucleation activities. Our results from the two-part study suggest the importance of local binding to heterogeneous nucleation as well as the possibility of using the binding affinity to the local area (the free energy of binding to the best site and the number of nucleating molecules associated with the area of the best binding site) and the distance order parameters to guide the selection of polymers.
Collapse
Affiliation(s)
- Surasak Chunsrivirot
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | |
Collapse
|
450
|
Rosa A, Orlandini E, Tubiana L, Micheletti C. Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology. Macromolecules 2011. [DOI: 10.1021/ma201827f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Angelo Rosa
- SISSA, Scuola Internazionale Superiore di Studi Avanzati and IIT, Italian Institute of Technology (SISSA unit), Via Bonomea 265, 34136 Trieste, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica and Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Luca Tubiana
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Cristian Micheletti
- SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|