1
|
Antón R, Treviño MÁ, Pantoja-Uceda D, Félix S, Babu M, Cabrita EJ, Zweckstetter M, Tinnefeld P, Vera AM, Oroz J. Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions. Nat Commun 2024; 15:1925. [PMID: 38431667 PMCID: PMC10908835 DOI: 10.1038/s41467-024-46236-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Abnormal trinucleotide repeat expansions alter protein conformation causing malfunction and contribute to a significant number of incurable human diseases. Scarce structural insights available on disease-related homorepeat expansions hinder the design of effective therapeutics. Here, we present the dynamic structure of human PHOX2B C-terminal fragment, which contains the longest polyalanine segment known in mammals. The major α-helical conformation of the polyalanine tract is solely extended by polyalanine expansions in PHOX2B, which are responsible for most congenital central hypoventilation syndrome cases. However, polyalanine expansions in PHOX2B additionally promote nascent homorepeat conformations that trigger length-dependent phase transitions into solid condensates that capture wild-type PHOX2B. Remarkably, HSP70 and HSP90 chaperones specifically seize PHOX2B alternative conformations preventing phase transitions. The precise observation of emerging polymorphs in expanded PHOX2B postulates unbalanced phase transitions as distinct pathophysiological mechanisms in homorepeat expansion diseases, paving the way towards the search of therapeutics modulating biomolecular condensates in central hypoventilation syndrome.
Collapse
Affiliation(s)
- Rosa Antón
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - Miguel Á Treviño
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - David Pantoja-Uceda
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain
| | - Sara Félix
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - María Babu
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Eurico J Cabrita
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München, 81377, Germany
| | - Andrés M Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München, 81377, Germany
| | - Javier Oroz
- Instituto de Química Física Blas Cabrera (IQF), CSIC, E-28006, Madrid, Spain.
| |
Collapse
|
2
|
Becht DC, Leavens MJ, Zeng B, Rothfuss MT, Briknarová K, Bowler BE. Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A. Biochemistry 2022; 61:767-784. [PMID: 35430812 PMCID: PMC9150713 DOI: 10.1021/acs.biochem.2c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the first ubiquitin-associated domain from HHR23A, UBA(1), was determined by X-ray crystallography at a 1.60 Å resolution, and its stability, folding kinetics, and residual structure under denaturing conditions have been investigated. The concentration dependence of thermal denaturation and size-exclusion chromatography indicate that UBA(1) is monomeric. Guanidine hydrochloride (GdnHCl) denaturation experiments reveal that the unfolding free energy, ΔGu°'(H2O), of UBA(1) is 2.4 kcal mol-1. Stopped-flow folding kinetics indicates sub-millisecond folding with only proline isomerization phases detectable at 25 °C. The full folding kinetics are observable at 4 °C, yielding a folding rate constant, kf, in the absence of a denaturant of 13,000 s-1 and a Tanford β-value of 0.80, consistent with a compact transition state. Evaluation of the secondary structure via circular dichroism shows that the residual helical structure in the denatured state is replaced by polyproline II structure as the GdnHCl concentration increases. Analysis of NMR secondary chemical shifts for backbone 15NH, 13CO, and 13Cα atoms between 4 and 7 M GdnHCl shows three islands of residual helical secondary structure that align in sequence with the three native-state helices. Extrapolation of the NMR data to 0 M GdnHCl demonstrates that helical structure would populate to 17-33% in the denatured state under folding conditions. Comparison with NMR data for a peptide corresponding to helix 1 indicates that this helix is stabilized by transient tertiary interactions in the denatured state of UBA(1). The high helical content in the denatured state, which is enhanced by transient tertiary interactions, suggests a diffusion-collision folding mechanism.
Collapse
Affiliation(s)
- Dustin C. Becht
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Baisen Zeng
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Michael T. Rothfuss
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Klára Briknarová
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| |
Collapse
|
3
|
Niitsu A, Egawa A, Ikeda K, Tachibana K, Fujiwara T. Veratridine binding to a transmembrane helix of sodium channel Na v1.4 determined by solid-state NMR. Bioorg Med Chem 2018; 26:5644-5653. [PMID: 30389410 DOI: 10.1016/j.bmc.2018.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 11/30/2022]
Abstract
The multi-step ligand action to a target protein is an important aspect when understanding mechanisms of ligand binding and discovering new drugs. However, structurally capturing such complex mechanisms is challenging. This is particularly true for interactions between large membrane proteins and small molecules. One such large membrane of interest is Nav1.4, a eukaryotic voltage-gated sodium channel. Domain 4 segment 6 (D4S6) of Nav1.4 is a transmembrane α-helical segment playing a key role in channel gating regulation, and is targeted by a neurotoxin, veratridine (VTD). VTD has been suggested to exhibit a two-step action to activate Nav1.4. Here, we determine the NMR structure of a selectively 13C-labeled peptide corresponding to D4S6 and its VTD binding site in lipid bilayers determined by using magic-angle spinning solid-state NMR. By 13C NMR, we obtain NMR structural constraints as 13C chemical shifts and the 1H-2H dipolar couplings between the peptide and deuterated lipids. The peptide backbone structure and its location with respect to the membrane are determined under the obtained NMR structural constraints aided by replica exchange molecular dynamics simulations with an implicit membrane/solvent system. Further, by measuring the 1H-2H dipolar couplings to monitor the peptide-lipid interaction, we identify a VTD binding site on D4S6. When superimposed to a crystal structure of a bacterial sodium channel NavRh, the determined binding site is the only surface exposed to the protein exterior and localizes beside the second-step binding site reported in the past. Based on these results, we propose that VTD initially binds to these newly-determined residues on D4S6 from the membrane hydrophobic domain, which induces the first-step channel opening followed by the second-step blocking of channel inactivation of Nav1.4. Our findings provide new detailed insights of the VTD action mechanism, which could be useful in designing new drugs targeting D4S6.
Collapse
Affiliation(s)
- Ai Niitsu
- RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ayako Egawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kazuo Tachibana
- School of Science, Department of Chemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
4
|
Kobayashi Y, Hoshino M, Kameda T, Kobayashi K, Akaji K, Inuki S, Ohno H, Oishi S. Use of a Compact Tripodal Tris(bipyridine) Ligand to Stabilize a Single-Metal-Centered Chirality: Stereoselective Coordination of Iron(II) and Ruthenium(II) on a Semirigid Hexapeptide Macrocycle. Inorg Chem 2018; 57:5475-5485. [PMID: 29634246 DOI: 10.1021/acs.inorgchem.8b00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fe(II)-coordinating hexapeptides containing three 2,2'-bipyridine moieties as side chains were designed and synthesized. A cyclic hexapeptide having three [(2,2'-bipyridin)-5-yl]-d-alanine (d-Bpa5) residues, in which d-Bpa5 and Gly are alternately arranged with 3-fold rotational symmetry, coordinated with Fe(II) to form a 1:1 octahedral Fe(II)-peptide complex with a single facial-Λ configuration of the metal-centered chirality. NMR spectroscopy and molecular dynamics simulations revealed that the Fe(II)-peptide complex has an apparent C3-symmetric conformations on the NMR time scale, while the peptide backbone is subject to dynamic conformational exchange between three asymmetric β/γ conformations and one C3-symmetric γ/γ/γ conformation. The semirigid cyclic hexapeptide preferentially arranged these conformations of the small octahedral Fe(II)-bipyridine complex, as well as the Ru(II) congener, to underpin the single configuration of the metal-centered chirality.
Collapse
Affiliation(s)
- Yuka Kobayashi
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center , National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi , Koutou-ku, Tokyo 135-0064 , Japan
| | - Kazuya Kobayashi
- Kyoto Pharmaceutical University , Yamashina-ku , Kyoto 607-8412 , Japan
| | - Kenichi Akaji
- Kyoto Pharmaceutical University , Yamashina-ku , Kyoto 607-8412 , Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| |
Collapse
|
5
|
Jebarupa B, Muralidharan M, Srinivasu BY, Mandal AK, Mitra G. Effect of altered solution conditions on tau conformational dynamics: Plausible implication on order propensity and aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:668-679. [DOI: 10.1016/j.bbapap.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/23/2023]
|
6
|
Mizuno A, Matsui K, Shuto S. From Peptides to Peptidomimetics: A Strategy Based on the Structural Features of Cyclopropane. Chemistry 2017. [PMID: 28632330 DOI: 10.1002/chem.201702119] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptidomimetics, non-natural mimicries of bioactive peptides, comprise an important class of drug molecules. The essence of the peptidomimetic design is to mimic the key conformation assumed by the bioactive peptides upon binding to their targets. Regulation of the conformation of peptidomimetics is important not only to enhance target binding affinity and selectivity, but also to confer cell-membrane permeability for targeting protein-protein interactions in cells. The rational design of peptidomimetics with suitable three-dimensional structures is challenging, however, due to the inherent flexibility of peptides and their dynamic conformational changes upon binding to the target biomolecules. In this Minireview, a three-dimensional structural diversity-oriented strategy based on the characteristic structural features of cyclopropane to address this challenging issue in peptidomimetic chemistry is described.
Collapse
Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka, 561-0825, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| |
Collapse
|
7
|
Mizuno A, Kameda T, Kuwahara T, Endoh H, Ito Y, Yamada S, Hasegawa K, Yamano A, Watanabe M, Arisawa M, Shuto S. Cyclopropane-Based Peptidomimetics Mimicking Wide-Ranging Secondary Structures of Peptides: Conformational Analysis and Their Use in Rational Ligand Optimization. Chemistry 2017; 23:3159-3168. [PMID: 28000361 DOI: 10.1002/chem.201605312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/16/2022]
Abstract
Detailed conformational analyses of our previously reported cyclopropane-based peptidomimetics and conformational analysis-driven ligand optimization are described. Computational calculations and X-ray crystallography showed that the characteristic features of cyclopropane function effectively to constrain the molecular conformation in a three-dimensionally diverse manner. Subsequent principal component analysis revealed that the diversity covers the broad chemical space filled by peptide secondary structures in terms of both main-chain and side-chain conformations. Based on these analyses, a lead stereoisomer targeting melanocortin receptors was identified, and its potency and subtype selectivity were improved by further derivatization. The presented strategy is effective not only for designing non-peptidic ligands from a peptide ligand but also for the rational optimization of these ligands based on the plausible target-binding conformation without requiring the three- dimensional structural information of the target and its peptide ligands.
Collapse
Affiliation(s)
- Akira Mizuno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Tomoshi Kameda
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7, Aomi, Koutou-ku, Tokyo, 135-0064, Japan
| | - Tomoki Kuwahara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Hideyuki Endoh
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yoshihiko Ito
- School of Pharmaceutical Sciences, University of Shizuoka, Yata, Suruga-ku, Shizuoka, Shizuoka, 422-8526, Japan
| | - Shizuo Yamada
- School of Pharmaceutical Sciences, University of Shizuoka, Yata, Suruga-ku, Shizuoka, Shizuoka, 422-8526, Japan
| | - Kimiko Hasegawa
- Rigaku Corporation, Application Laboratories, 3-9-12, Matsubara-cho, Akishima, Tokyo, 196-8666, Japan
| | - Akihito Yamano
- Rigaku Corporation, Application Laboratories, 3-9-12, Matsubara-cho, Akishima, Tokyo, 196-8666, Japan
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Mitsuhiro Arisawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| |
Collapse
|
8
|
Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| |
Collapse
|
9
|
Wang S, Otani Y, Liu X, Kawahata M, Yamaguchi K, Ohwada T. Robust trans-Amide Helical Structure of Oligomers of Bicyclic Mimics of β-Proline: Impact of Positional Switching of Bridgehead Substituent on Amide cis–trans Equilibrium. J Org Chem 2014; 79:5287-300. [DOI: 10.1021/jo500916j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Siyuan Wang
- Graduate School
of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuko Otani
- Graduate School
of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xin Liu
- Graduate School
of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masatoshi Kawahata
- Department of Pharmaceutical Sciences at
Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Kentaro Yamaguchi
- Department of Pharmaceutical Sciences at
Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomohiko Ohwada
- Graduate School
of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
10
|
Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
11
|
Collier G, Vellore NA, Yancey JA, Stuart SJ, Latour RA. Comparison between empirical protein force fields for the simulation of the adsorption behavior of structured LK peptides on functionalized surfaces. Biointerphases 2012; 7:24. [PMID: 22589067 DOI: 10.1007/s13758-012-0024-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 02/17/2012] [Indexed: 10/28/2022] Open
Abstract
All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results.
Collapse
Affiliation(s)
- Galen Collier
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA
| | | | | | | | | |
Collapse
|
12
|
Cruz VL, Ramos J, Martinez-Salazar J. Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results. J Phys Chem B 2011; 116:469-75. [PMID: 22136632 DOI: 10.1021/jp206757j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, α conformation-probabilities for all of the dipeptides remain much lower than either β or P(II) propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where α conformations result even more probable than P(II) or β ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.
Collapse
Affiliation(s)
- Victor L Cruz
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC Serrano 113-bis, Madrid, Spain.
| | | | | |
Collapse
|
13
|
Georgoulia PS, Glykos NM. Using J-coupling constants for force field validation: application to hepta-alanine. J Phys Chem B 2011; 115:15221-7. [PMID: 22087590 DOI: 10.1021/jp209597e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A computational solution to the protein folding problem is the holy grail of biomolecular simulation and of the corresponding force fields. The complexity of the systems used for folding simulations precludes a direct feedback between the simulations and the force fields, thus necessitating the study of simpler systems with sufficient experimental data to allow force field optimization and validation. Recent studies on short polyalanine peptides of increasing length (up to penta-alanine) indicated the presence of a systematic deviation between the experimental (NMR-derived) J-couplings and the great majority of biomolecular force fields, with the χ(2) values for even the best-performing force fields being in the 1.4-1.8 range. Here we show that by increasing the number of residues to seven and by achieving convergence through an increase of the simulation time to 2 μs, we can identify one force field (the AMBER99SB force field, out of the three force fields studied) which when compared with the experimental J-coupling data (and for a specific set of Karplus equation parameters and estimated J-coupling errors previously used in the literature) gave a value of χ(2) = 0.99, indicating that full statistical consistency between experiment and simulation is feasible. However, and as a detailed analysis of the effects of estimated errors shows, the χ(2) values may be unsuitable as indicators of the goodness of fit of the various biomolecular force fields.
Collapse
Affiliation(s)
- Panagiota S Georgoulia
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | | |
Collapse
|
14
|
Bernacki JP, Murphy RM. Length-dependent aggregation of uninterrupted polyalanine peptides. Biochemistry 2011; 50:9200-11. [PMID: 21932820 DOI: 10.1021/bi201155g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyalanine (polyA) is the third-most prevalent homopeptide repeat in eukaryotes, behind polyglutamine and polyasparagine. Abnormal expansion of the polyA repeat is linked to at least nine human diseases, and the disease mechanism likely involves enhanced length-dependent aggregation. Because of the simplicity of its side chain, polyA has been a favorite target of computational studies, and because of their tendency to fold into α-helix, peptides containing polyA-rich domains have been a popular experimental subject. However, experimental studies on uninterrupted polyA are very limited. We synthesized polyA peptides containing uninterrupted sequences of 7 to 25 alanines (A7 to A25) and characterized their length-dependent conformation and aggregation properties. The peptides were primarily disordered, with a modest component of α-helix that increased with increasing length. From measurements of mean distance spanned by the polyA segment, we concluded that physiological buffers are neutral solvents for shorter polyA peptides and poor solvents for longer peptides. At moderate concentration and near-physiological temperature, polyA assembled into soluble oligomers, with a sharp transition in oligomer physical properties between A19 and A25. With A19, oligomers were large, contained only a small fraction of the total peptide mass, and slowly grew into loose clusters, while A25 rapidly and completely assembled into small stable oligomers of ~7 nm radius. At high temperatures, A19 assembled into fibrils, but A25 precipitated as dense, micrometer-sized particles. A comparison of these results to those obtained with polyglutamine peptides of similar design sheds light on the role of the side chain in regulating conformation and aggregation.
Collapse
Affiliation(s)
- Joseph P Bernacki
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
| | | |
Collapse
|
15
|
Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B 2011; 115:9327-36. [DOI: 10.1021/jp205290t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Tomoshi Kameda
- Computational Biology Research Center, Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Erisa Harada
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Hideo Akutsu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 Japan
| |
Collapse
|
16
|
Mansiaux Y, Joseph AP, Gelly JC, de Brevern AG. Assignment of PolyProline II conformation and analysis of sequence--structure relationship. PLoS One 2011; 6:e18401. [PMID: 21483785 PMCID: PMC3069088 DOI: 10.1371/journal.pone.0018401] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 03/07/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Secondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein-protein interactions. METHODOLOGY/PRINCIPAL FINDINGS A major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined. CONCLUSIONS/SIGNIFICANCE The simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence-structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.
Collapse
Affiliation(s)
- Yohann Mansiaux
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Agnel Praveen Joseph
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Jean-Christophe Gelly
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Alexandre G. de Brevern
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Université Paris Diderot - Paris 7, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- * E-mail:
| |
Collapse
|
17
|
Ikebe J, Umezawa K, Kamiya N, Sugihara T, Yonezawa Y, Takano Y, Nakamura H, Higo J. Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. J Comput Chem 2010; 32:1286-97. [PMID: 21425286 DOI: 10.1002/jcc.21710] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 09/09/2010] [Accepted: 10/14/2010] [Indexed: 11/10/2022]
Abstract
Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.
Collapse
Affiliation(s)
- Jinzen Ikebe
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Chen Y, Ding J. Roles of non-native hydrogen-bonding interaction in helix-coil transition of a single polypeptide as revealed by comparison between Gō-like and non-Gō models. Proteins 2010; 78:2090-100. [PMID: 20455265 DOI: 10.1002/prot.22724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To explore the role of non-native interactions in the helix-coil transition, a detailed comparison between a Gō-like model and a non-Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō-like model, and the non-native ones with sequence interval more than 4 is also included into the non-Gō model. Some significant differences between the results from those two models have been found. The non-native hydrogen bonds were found most populated at temperature around the helix-coil transition. The rearrangement of non-native hydrogen bonds into native ones in the formation of alpha-helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non-Gō model for a non-short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non-native hydrogen bonds have complicated the temperature-dependence of Zimm-Bragg nucleation constant. The increase of relative probability of non-native hydrogen bonding for long polypeptide chains leads to non-monotonous chain length effect on the transition temperature.
Collapse
Affiliation(s)
- Yantao Chen
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
| | | |
Collapse
|
19
|
Hirano A, Kameda T, Arakawa T, Shiraki K. Arginine-Assisted Solubilization System for Drug Substances: Solubility Experiment and Simulation. J Phys Chem B 2010; 114:13455-62. [DOI: 10.1021/jp101909a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Atsushi Hirano
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Tomoshi Kameda
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Tsutomu Arakawa
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| | - Kentaro Shiraki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan, Computational Biology Research Center, Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan, and Alliance Protein Laboratories, Thousand Oaks, California 91360, United States
| |
Collapse
|
20
|
Yan Z, Wang J, Zhang J, Qin M, Wang W. Structural selection of ionic-complementary peptides with electrostatic interactions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:031917. [PMID: 21230118 DOI: 10.1103/physreve.82.031917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 06/21/2010] [Indexed: 05/30/2023]
Abstract
The structures of the peptides and their assembly are largely modulated by the environment. To discover the physical principles governing the structural modulations of peptides by the environment would be useful for many applications. As the typical examples, the structures of three kinds of ionic-complementary EAK16-family peptides under various environmental conditions are studied with simulations in this work. A model with intermediate resolution is used, in which both the backbone hydrogen bonds and electrostatic interactions are explicitly considered. The thermodynamics of these peptides (including the free energy and heat capacity) are described for various strengths of the electrostatic interactions which reflect the variation of environment. With these results, the phase diagrams of these peptides related to the temperature and the strength of electrostatic interactions are presented and compared. Based on the differences in the phase structures of the peptide, the different aggregation behaviors are explained based on the monomeric structural features of the peptides. Through the analysis on the stability of various secondary structures of these peptides, it is demonstrated that the charge pattern is the basic reason of the different responses of the EAK16-family peptides to the environmental changes. These results provide some examples and insights for the principles of structural selection by environment and may be helpful for further analysis and designs of peptide systems.
Collapse
Affiliation(s)
- Zhiqiang Yan
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | | | | | | | | |
Collapse
|
21
|
Computational approaches for the design of peptides with anti-breast cancer properties. Future Med Chem 2009; 1:201-12. [DOI: 10.4155/fmc.09.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.
Collapse
|
22
|
Jiang P, Xu W, Mu Y. Amyloidogenesis abolished by proline substitutions but enhanced by lipid binding. PLoS Comput Biol 2009; 5:e1000357. [PMID: 19360098 PMCID: PMC2663790 DOI: 10.1371/journal.pcbi.1000357] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 03/11/2009] [Indexed: 01/21/2023] Open
Abstract
The influence of lipid molecules on the aggregation of a highly amyloidogenic segment of human islet amyloid polypeptide, hIAPP20-29, and the corresponding sequence from rat has been studied by all-atom replica exchange molecular dynamics (REMD) simulations with explicit solvent model. hIAPP20-29 fragments aggregate into partially ordered beta-sheet oligomers and then undergo large conformational reorganization and convert into parallel/antiparallel beta-sheet oligomers in mixed in-register and out-of-register patterns. The hydrophobic interaction between lipid tails and residues at positions 23-25 is found to stabilize the ordered beta-sheet structure, indicating a catalysis role of lipid molecules in hIAPP20-29 self-assembly. The rat IAPP variants with three proline residues maintain unstructured micelle-like oligomers, which is consistent with non-amyloidogenic behavior observed in experimental studies. Our study provides the atomic resolution descriptions of the catalytic function of lipid molecules on the aggregation of IAPP peptides.
Collapse
Affiliation(s)
- Ping Jiang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
23
|
Abstract
We investigate the structures of the major folding transition states of nine proteins by correlation of published Phi-values with inter-residue contact maps. Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation-condensation mechanism with a concurrent build-up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the molecule and most intense in a single structural region suggesting the occurrence of a single folding nucleus. However, on average helix- and sheet-forming residues show somewhat larger Phi-values in the major transition state, suggesting that secondary structure formation is one important driving force in the nucleation-condensation in many proteins and that secondary-structure forming residues tend to be more prominent in folding nuclei. We synthesize the combined information on these 10 of 15 proteins into a unified nucleation-condensation mechanism which also accounts for effects described by the framework, hydrophobic collapse, zipper, and funnel models.
Collapse
Affiliation(s)
- Bengt Nölting
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158-2517, USA
| | | |
Collapse
|
24
|
Yamamoto T, Nair P, Jacobsen NE, Davis P, Ma SW, Navratilova E, Moye S, Lai J, Yamamura HI, Vanderah TW, Porreca F, Hruby VJ. The importance of micelle-bound states for the bioactivities of bifunctional peptide derivatives for delta/mu opioid receptor agonists and neurokinin 1 receptor antagonists. J Med Chem 2008; 51:6334-47. [PMID: 18821747 DOI: 10.1021/jm800389v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To provide new insight into the determining factors of membrane-bound peptide conformation that might play an important role in peptide-receptor docking and further biological behaviors, the dodecylphosphocholine (DPC) micelle-bound conformations of bifunctional peptide derivatives of delta-preferring opioid agonists and NK1 antagonists (1: Tyr-D-Ala-Gly-Phe-Met-Pro-Leu-Trp-O-3,5-Bzl(CF 3) 2; 2: Tyr-D-Ala-Gly-Phe-Met-Pro-Leu-Trp-NH-3,5-Bzl(CF 3) 2; 3: Tyr-D-Ala-Gly-Phe-Met-Pro-Leu-Trp-NH-Bzl) were determined based on 2D NMR studies. Although the differences in the primary sequence were limited to the C-terminus, the obtained NMR conformations were unexpectedly different for each compound. Moreover, their biological activities showed different trends in direct relation to the compound-specific conformations in DPC micelles. The important result is that not only were the NK1 antagonist activities different (the pharmacophore located at the C-terminus)but the opioid agonist activities (this pharmacophore was at the structurally preserved N-terminus) also were shifted, suggesting that a general conformational change in the bioactive state was induced due to relatively small and limited structural modifications.
Collapse
Affiliation(s)
- Takashi Yamamoto
- Department of Chemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Lemkul JA, Bevan DR. A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer. Arch Biochem Biophys 2007; 470:54-63. [PMID: 18053791 DOI: 10.1016/j.abb.2007.11.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 11/06/2007] [Accepted: 11/08/2007] [Indexed: 10/22/2022]
Abstract
Because the amyloid beta-peptide (Abeta) functions as approximately half of the transmembrane domain of the amyloid precursor protein and interaction of Abeta with membranes is proposed to result in neurotoxicity, the association of Abeta with membranes likely is important in the etiology of Alzheimer's disease. Atomic details of the interaction of Abeta with membranes are not accessible with most experimental techniques, but computational methods can provide this information. Here, we present the results of ten 100-ns molecular dynamics (MD) simulations of the 40-residue amyloid beta-peptide (Abeta40) embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer. The present study examines the effects of insertion depth, protonation state of key residues, and ionic strength on Abeta40 in a DPPC bilayer. In all cases, a portion of the peptide remained embedded in the bilayer. In the case of deeper insertion depth, Abeta40 adopted a near-transmembrane orientation, drawing water molecules into the bilayer to associate with its charged amino acids. In the case of shallower insertion, the most widely-accepted construct, the peptide associated strongly with the membrane-water interface and the phosphatidylcholine headgroups of the bilayer. In most cases, significant disordering of the extracellular segment of the peptide was observed, and the brief appearance of a beta-strand was noted in one case. Our results compare well with a variety of experimental and computational findings. From this study, we conclude that Abeta associated with membranes is dynamic and capable of adopting a number of conformations, each of which may have significance in understanding the progression of Alzheimer's disease.
Collapse
Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, West Campus Drive, 201 Fralin Biotechnology Center, Blacksburg, VA 24061, USA
| | | |
Collapse
|
26
|
Kirschner KN, Lexa KW, Salisburg AM, Alser KA, Joseph L, Andersen TT, Bennett JA, Jacobson HI, Shields GC. Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc 2007; 129:6263-8. [PMID: 17441722 PMCID: PMC4272344 DOI: 10.1021/ja070202w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Breast cancer is the most common cancer among women, and tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment. Many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Consequently, there is an ongoing need for breast cancer drugs that have different molecular targets. Previous work has shown that 8-mer and cyclic 9-mer peptides inhibit breast cancer in mouse and rat models, interacting with an unsolved receptor, while peptides smaller than eight amino acids did not. We show that the use of replica exchange molecular dynamics predicts the structure and dynamics of active peptides, leading to the discovery of smaller peptides with full biological activity. Simulations identified smaller peptide analogues with the same conserved reverse turn demonstrated in the larger peptides. These analogues were synthesized and shown to inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition.
Collapse
|
27
|
Lindberg MO, Oliveberg M. Malleability of protein folding pathways: a simple reason for complex behaviour. Curr Opin Struct Biol 2007; 17:21-9. [PMID: 17251003 DOI: 10.1016/j.sbi.2007.01.008] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 12/13/2006] [Accepted: 01/12/2007] [Indexed: 10/23/2022]
Abstract
Although the structures of native proteins are generally unique, the pathways by which they form are often free to vary. Some proteins fold by a multitude of different pathways, whereas others seem restricted to only one choice. An explanation for this variation in folding behaviour has recently emerged from studies of transition state changes: the number of accessible pathways is linked to the number of nucleation motifs contained within the native topology. We refer to these nucleation motifs as 'foldons', as they approach the size of an independent cooperative unit. Thus, with respect to pathway malleability and the composition of the folding funnel, proteins can be seen as modular assemblies of competing foldons. For the split beta-alpha-beta fold, these foldons are two-strand-helix motifs coupled by spatial overlap.
Collapse
Affiliation(s)
- Magnus O Lindberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | | |
Collapse
|