1
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Yang CT, Chu LK. Protein dynamics of human serum albumin at hypothermic temperatures investigated by temperature jump. Phys Chem Chem Phys 2022; 24:11079-11085. [PMID: 35471209 DOI: 10.1039/d2cp00220e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human serum albumin (HSA) is the most abundant protein in human plasma. Most protein dynamics studies of HSA have been performed above the hyperthermia temperature (>42 °C), so information on the dynamics under hypothermic conditions (<35 °C) is lacking. In this work, a tryptophan-based fluorescence temperature jump system was employed to investigate the thermally-induced dynamic process of HSA at a physiological concentration of ca. 45 mg mL-1 and pH = ca. 7 upon an instantaneous temperature increase from 25 °C to 30-43 °C. The observed kinetics manifested a three-state consecutive feature, . Upon analysis with the Arrhenius model, the rate coefficients k1 and k2 manifested piecewise temperature dependence, and the turning-point temperature was found to be ca. 34 °C, coinciding with the upper bound of hypothermic temperature. Meanwhile, the corresponding activation energies of the transitions at 34-43 °C were lower than those at 30-34 °C, suggesting that protein conformational adjustments at 34-43 °C were more feasible than those at hypothermic temperatures. These observations provided a fresh viewpoint on the relationship between the energetics of protein dynamics and the apparent functioning of a given protein at the molecular level.
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Affiliation(s)
- Chih-Tsun Yang
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan.
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan.
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2
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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3
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Directly monitor protein rearrangement on a nanosecond-to-millisecond time-scale. Sci Rep 2017; 7:8691. [PMID: 28821738 PMCID: PMC5562898 DOI: 10.1038/s41598-017-08385-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/10/2017] [Indexed: 11/09/2022] Open
Abstract
In order to directly observe the refolding kinetics from a partially misfolded state to a native state in the bottom of the protein-folding funnel, we used a "caging" strategy to trap the β-sheet structure of ubiquitin in a misfolded conformation. We used molecular dynamics simulation to generate the cage-induced, misfolded structure and compared the structure of the misfolded ubiquitin with native ubiquitin. Using laser flash irradiation, the cage can be cleaved from the misfolded structure within one nanosecond, and we monitored the refolding kinetics of ubiquitin from this misfolded state to the native state by photoacoustic calorimetry and photothermal beam deflection techniques on nanosecond to millisecond timescales. Our results showed two refolding events in this refolding process. The fast event is shorter than 20 ns and corresponds to the instant collapse of ubiquitin upon cage release initiated by laser irradiation. The slow event is ~60 μs, derived from a structural rearrangement in β-sheet refolding. The event lasts 10 times longer than the timescale of β-hairpin formation for short peptides as monitored by temperature jump, suggesting that rearrangement of a β-sheet structure from a misfolded state to its native state requires more time than ab initio folding of a β-sheet.
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4
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Kang CH, Lee YM, Park JH, Nawkar GM, Oh HT, Kim MG, Lee SI, Kim WY, Yun DJ, Lee SY. Ribosomal P3 protein AtP3B of Arabidopsis acts as both protein and RNA chaperone to increase tolerance of heat and cold stresses. PLANT, CELL & ENVIRONMENT 2016; 39:1631-42. [PMID: 27004478 DOI: 10.1111/pce.12742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 05/16/2023]
Abstract
The P3 proteins are plant-specific ribosomal P-proteins; however, their molecular functions have not been characterized. In a screen for components of heat-stable high-molecular weight (HMW) complexes, we isolated the P3 protein AtP3B from heat-treated Arabidopsis suspension cultures. By size-exclusion chromatography (SEC), SDS-PAGE and native PAGE followed by immunoblotting with anti-AtP3B antibody, we showed that AtP3B was stably retained in HMW complexes following heat shock. The level of AtP3B mRNA increased in response to both high- and low-temperature stresses. Bacterially expressed recombinant AtP3B protein exhibited both protein and RNA chaperone activities. Knockdown of AtP3B by RNAi made plants sensitive to both high- and low-temperature stresses, whereas overexpression of AtP3B increased tolerance of both conditions. Together, our results suggest that AtP3B protects cells against both high- and low-temperature stresses. These findings provide novel insight into the molecular functions and in vivo roles of acidic ribosomal P-proteins, thereby expanding our knowledge of the protein production machinery.
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Affiliation(s)
- Chang Ho Kang
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Young Mee Lee
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
- Genetics and Breeding Research Center, NFRDI, Geoje, 656-842, Korea
| | - Joung Hun Park
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Ganesh M Nawkar
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hun Taek Oh
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea
| | - Woe Yeon Kim
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21+) and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea
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5
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Orevi T, Rahamim G, Amir D, Kathuria S, Bilsel O, Matthews CR, Haas E. Sequential Closure of Loop Structures Forms the Folding Nucleus during the Refolding Transition of the Escherichia coli Adenylate Kinase Molecule. Biochemistry 2015; 55:79-91. [DOI: 10.1021/acs.biochem.5b00849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Tomer Orevi
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Gil Rahamim
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Dan Amir
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
| | - Sagar Kathuria
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Osman Bilsel
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - C. Robert Matthews
- Department
of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Elisha Haas
- The
Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel 52900
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6
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Sugita M, Matsuoka M, Kikuchi T. Topological and sequence information predict that foldons organize a partially overlapped and hierarchical structure. Proteins 2015; 83:1900-13. [PMID: 26248725 DOI: 10.1002/prot.24874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/23/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022]
Abstract
It has been suggested that proteins have substructures, called foldons, which can cooperatively fold into the native structure. However, several prior investigations define foldons in various ways, citing different foldon characteristics, thereby making the concept of a foldon ambiguous. In this study, we perform a Gō model simulation and analyze the characteristics of substructures that cooperatively fold into the native-like structure. Although some results do not agree well with the experimental evidence due to the simplicity of our coarse-grained model, our results strongly suggest that cooperatively folding units sometimes organize a partially overlapped and hierarchical structure. This view makes us easy to interpret some different proposal about the foldon as a difference of the hierarchical structure. On the basis of this finding, we present a new method to assign foldons and their hierarchy, using structural and sequence information. The results show that the foldons assigned by our method correspond to the intermediate structures identified by some experimental techniques. The new method makes it easy to predict whether a protein folds sequentially into the native structure or whether some foldons fold into the native structure in parallel.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Masanari Matsuoka
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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7
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Panman MR, van Dijk CN, Meuzelaar H, Woutersen S. Communication: Nanosecond folding dynamics of an alpha helix: Time-dependent 2D-IR cross peaks observed using polarization-sensitive dispersed pump-probe spectroscopy. J Chem Phys 2015; 142:041103. [DOI: 10.1063/1.4906456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthijs R. Panman
- Van ’t Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Chris N. van Dijk
- Van ’t Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Heleen Meuzelaar
- Van ’t Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - S. Woutersen
- Van ’t Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
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8
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Naganathan AN, Sanchez-Ruiz JM, Munshi S, Suresh S. Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints? J Phys Chem B 2015; 119:1323-33. [DOI: 10.1021/jp510342m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica,
Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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9
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Abstract
Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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10
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Naganathan AN, Muñoz V. Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier. J Phys Chem B 2014; 118:8982-94. [DOI: 10.1021/jp504261g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Athi N. Naganathan
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Victor Muñoz
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Centro Nacional
de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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11
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Narayan A, Naganathan AN. Evidence for the sequential folding mechanism in RNase H from an ensemble-based model. J Phys Chem B 2014; 118:5050-8. [PMID: 24762044 DOI: 10.1021/jp500934f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of distinct protein folding pathways starting from an unfolded ensemble, and hence, the folding mechanism is an intricate function of protein size, sequence complexity, and stability conditions. This has traditionally been a contentious issue particularly because of the ensemble nature of conventional experiments that can mask the complexity of the underlying folding landscape. Recent hydrogen-exchange experiments combined with mass spectrometry (HX-MS) reveal that the folding of RNase H proceeds in a hierarchical fashion with distinct intermediates and following a single discrete path. In our current work, we provide computational evidence for this unique folding mechanism by employing a structure-based statistical mechanical model. Upon calibrating the energetic terms of the model with equilibrium measurements, we predict multiple intermediate states in the folding of RNase H that closely resemble experimental observations. Remarkably, a simplified landscape representation adequately captures the folding complexity and predicts the possibility of a well-defined sequence of folding events. We supplement the statistical model study with both explicit solvent molecular simulations of the helical units and electrostatic calculations to provide structural and energetic insights into the early and late stages of RNase H folding that hint at the frustrated nature of its folding landscape.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
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12
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. Biopolymers 2014; 101:536-48. [DOI: 10.1002/bip.22416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/05/2013] [Accepted: 09/16/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin A. Anderson
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Alex Literati
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Borden Ball
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
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13
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Davis CM, Dyer RB. Dynamics of an ultrafast folding subdomain in the context of a larger protein fold. J Am Chem Soc 2013; 135:19260-7. [PMID: 24320936 PMCID: PMC3949483 DOI: 10.1021/ja409608r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small fast folding subdomains with low contact order have been postulated to facilitate the folding of larger proteins. We have tested this idea by determining how the fastest folding linear β-hairpin, CLN025, which folds on the nanosecond time scale, folds within the context of a two-hairpin WW domain system, which folds on the microsecond time scale. The folding of the wild type FBP28 WW domain was compared to constructs in which each of the loops was replaced by CLN025. A combination of FTIR spectroscopy and laser-induced temperature-jump coupled with infrared spectroscopy was used to probe changes in the peptide backbone. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding bands assigned in the amide I region. The folding rate of the CLN025 β-hairpin is unchanged within the larger protein. Insertion of the β-hairpin into the second loop results in an overall stabilization of the WW domain and a relaxation lifetime five times faster than the parent WW domain. In both mutants, folding is initiated in the turns and the β-sheets form last. These results demonstrate that fast folding subdomains can be used to speed the folding of more complex proteins, and that the folding dynamics of the subdomain is unchanged within the context of the larger protein.
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Affiliation(s)
- Caitlin M. Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - R. Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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14
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Sugita M, Kikuchi T. Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: relationship between the free energy profiles and folding cores. Proteins 2013; 82:954-65. [PMID: 24214655 DOI: 10.1002/prot.24469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/30/2013] [Accepted: 10/29/2013] [Indexed: 11/07/2022]
Abstract
The folding mechanisms of proteins with multi-state transitions, the role of the intermediate states, and the precise mechanism how each transition occurs are significant on-going research issues. In this study, we investigate ferredoxin-like fold proteins which have a simple topology and multi-state transitions. We analyze the folding processes by means of a coarse-grained Gō model. We are able to reproduce the differences in the folding mechanisms between U1A, which has a high-free-energy intermediate state, and ADA2h and S6, which fold into the native structure through two-state transitions. The folding pathways of U1A, ADA2h, S6, and the S6 circular permutant, S6_p54-55, are reproduced and compared with experimental observations. We show that the ferredoxin-like fold contains two common regions consisting folding cores as predicted in other studies and that U1A produces an intermediate state due to the distinct cooperative folding of each core. However, because one of the cores of S6 loses its cooperativity and the two cores of ADA2h are tightly coupled, these proteins fold into the native structure through a two-state mechanism.
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Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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15
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Kubelka J. Multivariate Analysis of Spectral Data with Frequency Shifts: Application to Temperature Dependent Infrared Spectra of Peptides and Proteins. Anal Chem 2013; 85:9588-95. [DOI: 10.1021/ac402083p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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16
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Sugita M, Kikuchi T. Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations. Proteins 2013; 81:1434-45. [DOI: 10.1002/prot.24294] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/13/2013] [Accepted: 03/17/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Masatake Sugita
- Department of Bioinformatics; College of Life Sciences; Ritsumeikan University; Kusatsu; Shiga; Japan
| | - Takeshi Kikuchi
- Department of Bioinformatics; College of Life Sciences; Ritsumeikan University; Kusatsu; Shiga; Japan
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