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Brookhaven Postoctoral Position

Postdoctoral Research Associate Macromolecular Crystallography
Job ID 2729 Date posted 07/26/2021

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Brookhaven National Laboratory (www.bnl.gov) delivers discovery science and transformative technology to power and secure the nation's future. Brookhaven Lab is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and more than 70 years of pioneering research. The Lab is primarily supported by the U.S. Department of Energy's (DOE) Office of Science. Brookhaven Science Associates (BSA) operates and manages the Laboratory for DOE. BSA is a partnership between Battelle and The Research Foundation for the State University of New York on behalf of Stony Brook University.

Organizational Overview

Brookhaven National Laboratory is entering an exciting new chapter with one of the newest and most advanced synchrotron facilities in the world. National Synchrotron Light Source II (NSLS-II) enables the study of material properties and functions with nanoscale resolution and exquisite sensitivity by providing world-leading capabilities for X-ray imaging and high-resolution energy analysis.

This facility is open to users from academia and industry and its operations are at a time when the world enters a new era with a global economy fueled largely by scientific discoveries and technological innovations. NSLS-II provides the research tools needed to foster new discoveries and create breakthroughs in critical areas such as energy security, environment, and human health.

Position Description

The Center for BioMolecular Structure at the National Synchrotron Light Source-II (NSLS-II) at Brookhaven National Laboratory seeks a postdoctoral research associate to join our program that operates two state-of-the-art macromolecular crystallography (MX) beamlines, a life-sciences scattering beamline, and a cryo-EM facility. The successful researcher who joins our multi-national multi-disciplinary team will expand the scientific capabilities of the Frontier Macromolecular Crystallography (FMX) beamline's unsurpassed brightness and micro-focus beam. The project will establish room temperature and time-resolved serial synchrotron crystallography at the FMX beamline, in a close collaboration with our colleagues at the BNL Biology department, with the goal to study dynamic processes in proteins such as enzymatic reactions. The position is a two-year term appointment.

Essential Duties and Responsibilities:

Study dynamic and time resolved processes in proteins with a fixed-target chip-scanning goniometer at FMX.
Develop a fixed-target sample holder, room temperature sample handling protocols and a reaction trigger mechanism.
Design the time-resolved serial synchrotron crystallography (SSX) experiment and associated data analysis.
Successful structure solutions of reaction intermediates will provide new insights into protein function.

Position Requirements

Required Knowledge, Skills, and Abilities:

Ph.D. in chemistry, biochemistry, physics, biophysics, or a related field
Demonstrated background in Macromolecular Crystallography data acquisition and analysis
Demonstrated publication record in X-ray or neutron-based research
Excellent oral and written communication skills and effective interaction in a team environment

Preferred Knowledge, Skills, and Abilities:

Experience in the use of synchrotron beamlines for structural biology
Experience in protein purification and sample preparation for structural analysis
Interest or skills in instrument development, particularly in liquid handling
Experience with programming
Experience in scientific computation and large-scale data processing

BNL policy requires that research associate appointments be made to individuals who have received their doctorate within the past five years .

At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes, but is not limited to:

Medical, Dental, and Vision Care Plans
Flexible Spending Account
Paid Time-off and Leave Programs (vacation, holidays, sick leave, paid parental leave)
401(k) Plan
Flexible Work Arrangements
Tuition Assistance, Training and Professional Development Programs
Employee Fitness/Wellness & Recreation: Gym/Basketball Courts, Weight Room, Fitness Classes, Indoor Pool, Tennis Courts, Sports Clubs/Activities (Basketball, Ping Pong, Softball, Tennis)

Brookhaven National Laboratory and the Energy and Photon Sciences Directorate are committed to your success. We offer a supportive work environment and the resources necessary for you to succeed.
Brookhaven Science Associates requires proof of a COVID-19 vaccination for all employees.Proof of full vaccination as recognized by the CDC and/or WHO, inclusive of the two-week waiting period, is required either by November 17, 2021 or at the start of your employment if after November 17, 2021.

Brookhaven National Laboratory (BNL) is an equal opportunity employer that values inclusion and diversity at our Lab.We are committed to ensuring that all qualified applicants receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, status as a veteran, disability or any other federal, state or local protected class.

BNL takes affirmative action in support of its policy and to advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities.We ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment.Please contact us to request accommodation.

*VEVRAA Federal Contractor

Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1A. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at: https://www.directives.doe.gov/directives-documents/400-series/0486.1-BOrder-a/@@images/file 

Graduate Studies at UB

PhD position in NMR-based structural enzymology combining NMR, SAXS and XFEL

SUNY Buffalo

Laboratory of Dr. Szyperski, Chemistry Department

BioXFEL STC funded project pursued in collaboration with

Drs. Edward Snell (HWI), Thomas Weiss (Stanford) and Marius Schmidt (UWM)

Research. Enzyme function is potentially linked to the entire protein conformational space sampled by enzyme and enzyme-intermediate complexes during catalysis. Importantly, this holds for lowly populated conformational sub-spaces of higher free energy, which can differ distinctly from the lowest free energy conformational sub-space typically captured in X-ray crystal and NMR structures. For large enzymatic ‘machines’, the most prominent example being the ribosome, FRET and cryo-EM have revealed the functional importance of large-scale conformational changes during substrate turnover. However, it is unknown to which extent large conformational changes associated with turnover typically exist for medium-sized enzymes, and if they are functionally important.

To address this question, our research focuses on the 29 kDa broad-spectrum
b-lactamase (BlaC) from Mycobacterium tuberculosis, a bacterial pathogen which causes worldwide ~1.5 million tuberculosis deaths each year. This enzyme is of outstanding biomedical importance because it conveys resistance [1] against b-lactam antibiotics (including the cephalosporin CEF) and greatly impedes antibiotic treatment of tuberculosis. Specifically, BlaCs hydrolyze b-lactam antibiotics and the detailed understanding of the enzymatic mechanism is of key importance to tackle antibiotic resistance.

This project focusses on the structural enzymology of BlaC combing new insights from solution nuclear magnetic resonance (NMR) spectroscopy, solution small angle X-ray scattering, and crystal X-ray scattering using free electron lasers (XFELs). Our unprecedented NMR and SAXS studies revealed the presence of large conformational excursions of the medium-sized BlaC during substrate turnover. In contrast, well resolved crystal structures were obtained for BlaC as well as catalytic intermediates in the pioneering Mix-and-Inject Serial (MISC) X-ray free electron laser (XFEL) studies of Schmidt and coworkers [1]. The central hypothesis driving our research is that the NMR-detected large excursions may well be of functional importance but are suppressed when the reaction proceeds in crystals. We received a grant for beamtime at the Stanford synchrotron to next perform time-resolved SAXS in order to (i) complement MISC and (ii) refine further structure-based models of the catalytic cycle.

Furthermore, we (i) characterized both competitive and non-competitive product inhibition by NMR chemical shift perturbation, and (ii) accurately measured BlaC Michaelis-Menten (MM) parameters and inhibition constants. To overcome limitations arising from fitting competitive and non-competitive inhibition from initial reaction velocities, we plan to fit our data using the integrated form of the Michaelis-Menten equation. Such fitting does not rely on the initial rate approximation and a form which considers simultaneous competitive and non-competitive inhibition is available [2]. We collaborate with Dr. Bezerra, who implemented the required non-linear fitting in the Solver Supplement of the Microsoft Office Excel program [3] and have tested this approach with our data.

Education and Training. This research project is exceptionally well-suited for cross-interdisciplinary training of PhD students in routine molecular biology for protein sample preparation, biophysics, NMR-based structural biology and advanced enzymology. This includes training in NMR, SAXS, and Xray crystallography, as well as circular dichroism and fluorescence spectroscopy molecular dynamics simulations

The successful candidate will be a PHD Student in the Chemistry Department of SUNY-Buffalo (UB) (https://arts-sciences.buffalo.edu/chemistry/graduate/overview/phd.html) and is expected to play an active role as a Teaching Assistant (TA). The student will be supported financially through the appointment as TA, research funding and possibly a scholarship.

Dr. Szyperski integrates novel research insights into his elective, special topic graduate course CHE 512 and organizes outreach biophysics webinars. The student will participate in our regular research meetings with collaborators, which includes meetings for our second NSF-funded project on the engineering of cold denaturing proteins.

Furthermore, the student will participate in the educational program of the BioXFEL STC (https://www.bioxfel.org/education), which was described by Dr. Bauer in a recent article [4], as a BioXFEL scholar (https://www.bioxfel.org/education/bioxfel-scholars/scholar-programs).

 

Interested students are welcome to send their CV along with a concise personal statement describing previous research experience and current research interests to Dr. Szyperski. He will then set up a Zoom meeting to become acquainted and to discuss opportunities.

 

Contact information

Thomas Szyperski

UB Distinguished Professor

Chemistry Department

University at Buffalo (UB)

This email address is being protected from spambots. You need JavaScript enabled to view it.

http://chemistry.buffalo.edu/people/szyperski

 

References

[1] Olmos, J.L. et al. Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography. BMC Biology, 2018, 16: 59.

[2] Bezerra, R. M. et al. Utilization of integrated Michaelis‐Menten equation to determine kinetic constants. Biochemistry and Molecular Biology Education 2007, 35: 145.

[3] Bezerra, R. M. et al. Utilization of integrated Michaelis–Menten equations for enzyme inhibition diagnosis and determination of kinetic constants using Solver supplement of Microsoft Office Excel. Computer Methods and Programs in Biomedicine 2013, 109, 26.

[4] Bauer, W. J., Woodruff, S. B. A science education model for large collaborative centers. Struct Dyn, 2021, 8: 020402.

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