Lee Makowski

Lee Makowski

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Lee Makowski

Lee Makowski

Publications by authors named "Lee Makowski"

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Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state.

Biochim Biophys Acta Gen Subj 2020 Mar 26:129604. Epub 2020 Mar 26.

Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, United States of America; Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.bbagen.2020.129604DOI Listing
March 2020

FiXR: a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments.

Acta Crystallogr D Struct Biol 2020 Feb 24;76(Pt 2):102-117. Epub 2020 Jan 24.

Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1107/S2059798319015961DOI Listing
February 2020

The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin.

Structure 2019 11 5;27(11):1647-1659.e4. Epub 2019 Sep 5.

Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.str.2019.08.009DOI Listing
November 2019

Predicting X-ray solution scattering from flexible macromolecules.

Protein Sci 2018 12 16;27(12):2023-2036. Epub 2018 Oct 16.

Department of Bioengineering, Northeastern University, Boston, Massachusetts.

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http://dx.doi.org/10.1002/pro.3508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237699PMC
December 2018

What Can We Learn from Wide-Angle Solution Scattering?

Adv Exp Med Biol 2017 ;1009:131-147

Northeastern University, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1007/978-981-10-6038-0_8DOI Listing
June 2018

Differential Enzyme Flexibility Probed Using Solid-State Nanopores.

ACS Nano 2018 05 17;12(5):4494-4502. Epub 2018 Apr 17.

Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States.

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http://dx.doi.org/10.1021/acsnano.8b00734DOI Listing
May 2018

Fine structure of conformational ensembles in adenylate kinase.

Proteins 2018 03 26;86(3):332-343. Epub 2017 Dec 26.

Department of Bioengineering, Northeastern University, Boston, Massachusetts.

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http://dx.doi.org/10.1002/prot.25443DOI Listing
March 2018

Calculation of the cross-sectional shape of a fibril from equatorial scattering.

J Struct Biol 2017 12 13;200(3):248-257. Epub 2017 May 13.

Northeastern University, Boston, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2017.05.003DOI Listing
December 2017

Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase.

Biochemistry 2017 08 16;56(34):4559-4567. Epub 2017 Aug 16.

Department of Bioengineering, Northeastern University , Boston, Massachusetts 02115, United States.

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http://dx.doi.org/10.1021/acs.biochem.7b00351DOI Listing
August 2017

Modulation of hemoglobin dynamics by an allosteric effector.

Protein Sci 2017 03 14;26(3):505-514. Epub 2017 Feb 14.

Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439.

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http://dx.doi.org/10.1002/pro.3099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326564PMC
March 2017

Rice Cellulose SynthaseA8 Plant-Conserved Region Is a Coiled-Coil at the Catalytic Core Entrance.

Plant Physiol 2017 01 22;173(1):482-494. Epub 2016 Nov 22.

Department of Biological Sciences (P.S.R., C.N.S., N.C.C., C.V.S.), Department of Botany and Plant Pathology (A.T.O., N.C.C.), Bindley Bioscience Center (N.C.C., C.V.S.), and Purdue Center for Cancer Research (C.V.S.), Purdue University, West Lafayette, Indiana 47907;

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http://dx.doi.org/10.1104/pp.16.00739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210708PMC
January 2017

Utility of Solution X-Ray Scattering for the Development of Antibody Biopharmaceuticals.

J Pharm Sci 2016 11 13;105(11):3278-3289. Epub 2016 Sep 13.

Department of Electrical and Computer Engineering, Northeastern University College of Engineering, Boston, Massachusetts 02115; Department of Chemistry and Chemical Engineering, Northeastern University, Boston, Massachusetts 02115. Electronic address:

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http://dx.doi.org/10.1016/j.xphs.2016.07.021DOI Listing
November 2016

c-Abl Tyrosine Kinase Adopts Multiple Active Conformational States in Solution.

Biochemistry 2016 06 3;55(23):3251-60. Epub 2016 Jun 3.

Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15219, United States.

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http://dx.doi.org/10.1021/acs.biochem.6b00202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910136PMC
June 2016

The impact of alterations in lignin deposition on cellulose organization of the plant cell wall.

Biotechnol Biofuels 2016 17;9:126. Epub 2016 Jun 17.

Department of Bioengineering, Northeastern University, 360 Huntington Ave, Boston, MA 02148 USA ; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02148 USA.

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http://dx.doi.org/10.1186/s13068-016-0540-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912819PMC
June 2016

Visualizing global properties of a molecular dynamics trajectory.

Proteins 2016 Jan 23;84(1):82-91. Epub 2015 Nov 23.

Department of Bioengineering, Northeastern University, Boston, Massachusetts.

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http://dx.doi.org/10.1002/prot.24957DOI Listing
January 2016

Modulation of HIV protease flexibility by the T80N mutation.

Proteins 2015 Nov 29;83(11):1929-39. Epub 2015 Sep 29.

Department of Bioengineering, Northeastern University, Boston, Massachusetts.

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http://dx.doi.org/10.1002/prot.24737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461556PMC
November 2015

Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements.

IEEE Trans Signal Process 2015 Oct 13;63(20):5383-5394. Epub 2015 Jul 13.

Bioengineering Department, Northeastern University, Boston, MA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA.

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http://dx.doi.org/10.1109/TSP.2015.2455515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767180PMC
October 2015

Breakdown of hierarchical architecture in cellulose during dilute acid pretreatments.

Cellulose (Lond) 2015;22(3):1495-1504. Epub 2015 Feb 28.

Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA ; Department of Bioengineering, Northeastern University, Boston, MA 02115 USA.

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http://dx.doi.org/10.1007/s10570-015-0592-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579859PMC
February 2015

The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers.

Plant Cell 2014 Jul 10;26(7):2996-3009. Epub 2014 Jul 10.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054 Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971 Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907-2057

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http://www.plantcell.org/content/early/2014/07/10/tpc.114.12
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http://www.plantcell.org/lookup/doi/10.1105/tpc.114.126862
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http://dx.doi.org/10.1105/tpc.114.126862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145127PMC
July 2014

Multiscale deconstruction of molecular architecture in corn stover.

Sci Rep 2014 Jan 20;4:3756. Epub 2014 Jan 20.

1] Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115 [2] Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115.

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http://dx.doi.org/10.1038/srep03756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895879PMC
January 2014

Investigating monoclonal antibody aggregation using a combination of H/DX-MS and other biophysical measurements.

J Pharm Sci 2013 Dec 17;102(12):4315-29. Epub 2013 Oct 17.

Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115.

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https://linkinghub.elsevier.com/retrieve/pii/S00223549153081
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http://dx.doi.org/10.1002/jps.23754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970822PMC
December 2013

Tissue specific specialization of the nanoscale architecture of Arabidopsis.

J Struct Biol 2013 Nov 26;184(2):103-14. Epub 2013 Sep 26.

Department of Electrical and Computer Engineering, Northeastern University, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2013.09.013DOI Listing
November 2013

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

J Chem Phys 2012 Sep;137(12):124101

Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612, USA.

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http://aip.scitation.org/doi/10.1063/1.4752735
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http://dx.doi.org/10.1063/1.4752735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3470608PMC
September 2012

X-ray coherent diffraction imaging of cellulose fibrils in situ.

Conf Proc IEEE Eng Med Biol Soc 2011 ;2011:528-30

Argonne National Laboratory.

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http://ieeexplore.ieee.org/document/6090096/
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http://dx.doi.org/10.1109/IEMBS.2011.6090096DOI Listing
June 2012

Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.

Biophys J 2011 Oct;101(8):2061-9

Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1016/j.bpj.2011.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192974PMC
October 2011

X-ray solution scattering studies of the structural diversity intrinsic to protein ensembles.

Biopolymers 2011 Aug 1;95(8):531-42. Epub 2011 Apr 1.

Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA.

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http://doi.wiley.com/10.1002/bip.21631
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http://dx.doi.org/10.1002/bip.21631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103594PMC
August 2011

Multidomain assembled states of Hck tyrosine kinase in solution.

Proc Natl Acad Sci U S A 2010 Sep 23;107(36):15757-62. Epub 2010 Aug 23.

Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1004569107
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http://dx.doi.org/10.1073/pnas.1004569107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936629PMC
September 2010

Modeling the hydration layer around proteins: HyPred.

Biophys J 2010 Sep;99(5):1611-9

Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000634951000739
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http://dx.doi.org/10.1016/j.bpj.2010.06.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931753PMC
September 2010

Characterization of proteins with wide-angle X-ray solution scattering (WAXS).

Authors:
Lee Makowski

J Struct Funct Genomics 2010 Mar 5;11(1):9-19. Epub 2010 Jan 5.

Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.

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http://dx.doi.org/10.1007/s10969-009-9075-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057577PMC
March 2010

Neutron spin-echo studies of hemoglobin and myoglobin: multiscale internal dynamics.

J Mol Biol 2010 Mar 22;397(2):423-35. Epub 2010 Jan 22.

Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.01.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850062PMC
March 2010

Simulated x-ray scattering of protein solutions using explicit-solvent models.

J Chem Phys 2009 Apr;130(13):134114

Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.

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http://dx.doi.org/10.1063/1.3099611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852435PMC
April 2009

Characterization of protein fold by wide-angle X-ray solution scattering.

J Mol Biol 2008 Nov 23;383(3):731-44. Epub 2008 Aug 23.

Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1016/j.jmb.2008.08.038DOI Listing
November 2008

Molecular crowding inhibits intramolecular breathing motions in proteins.

J Mol Biol 2008 Jan 17;375(2):529-46. Epub 2007 Aug 17.

Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4845, USA.

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http://dx.doi.org/10.1016/j.jmb.2007.07.075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2219890PMC
January 2008

Trinucleotide cassettes increase diversity of T7 phage-displayed peptide library.

BMC Biotechnol 2007 Oct 5;7:65. Epub 2007 Oct 5.

Molecular Targets Development Program, Center for Cancer Research, NCI-Frederick, Frederick, Maryland 21702, USA.

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http://dx.doi.org/10.1186/1472-6750-7-65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174457PMC
October 2007

Detection of functional ligand-binding events using synchrotron x-ray scattering.

J Biomol Screen 2007 Oct;12(7):994-8

Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439,USA.

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http://dx.doi.org/10.1177/1087057107306104DOI Listing
October 2007

Subtractive transcriptomics: establishing polarity drives in vitro human endothelial morphogenesis.

Cancer Res 2006 Apr;66(8):4030-40

Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-05-3294DOI Listing
April 2006

Phage display reveals multiple contact sites between FhuA, an outer membrane receptor of Escherichia coli, and TonB.

J Mol Biol 2006 Mar 27;357(1):236-51. Epub 2005 Dec 27.

Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Que., Canada H3A 2B4.

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http://dx.doi.org/10.1016/j.jmb.2005.12.039DOI Listing
March 2006

DIVAA: analysis of amino acid diversity in multiple aligned protein sequences.

Bioinformatics 2004 Dec 29;20(18):3481-9. Epub 2004 Jul 29.

Combinatorial Biology Unit, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth432DOI Listing
December 2004

RELIC--a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites.

Proteomics 2004 May;4(5):1439-60

Biociences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1002/pmic.200300680DOI Listing
May 2004

Genome-wide characterisation of the binding repertoire of small molecule drugs.

Hum Genomics 2003 Nov;1(1):41-51

Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525004PMC
http://dx.doi.org/10.1186/1479-7364-1-1-41DOI Listing
November 2003

High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrity.

J Synchrotron Radiat 2003 Sep 28;10(Pt 5):398-404. Epub 2003 Aug 28.

GM/CA-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1107/s0909049503016583DOI Listing
September 2003

Estimating the diversity of peptide populations from limited sequence data.

Bioinformatics 2003 Mar;19(4):483-9

Bioscience Division, Argonne National Laboratory, 9700 S. Cass Avenue Argonne, Illinois 60439, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg013DOI Listing
March 2003

Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries.

J Mol Biol 2002 Oct;322(5):1039-52

Combinatorial Biology Unit, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

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http://dx.doi.org/10.1016/s0022-2836(02)00844-6DOI Listing
October 2002

One from column A and two from column B: the benefits of phage display in molecular-recognition studies.

Curr Opin Chem Biol 2002 Feb;6(1):92-6

Combinatorial Biology Unit, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.

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http://dx.doi.org/10.1016/s1367-5931(01)00287-3DOI Listing
February 2002