Conference Proceeding for PROTEIN STRUCTURE AND DYNAMICS IN HEALTH AND ...

104 Pages·2012·3.79 MB·English

J P P JOURNAL OF PROTEINS AND PROTEOMICS
ISSN : 0975-8151: 8(4), 2017
SPECIAL ISSUE ON
PROTEIN STRUCTURE AND DYNAMICS IN
HEALTH AND AGRICULTURE
CONTENTS
Welcome Message by Editor in Chief, JPP
PART A : CONFERENCE PROCEEDINGS
Conference details, Organizing Committee, Advisory Board
About Jamia Millia Islamia (JMI), Department of Biosciences and Centre for Interdisciplinary
Research in Basic Sciences (CIRBSc)
Message from Vice Chancellor, JMI
Message from Chairman of Conference
Message from President of Protein Society
Message from Convenor of Conference
Programme Details
Abstracts for Keynote, Plenary and Invited Lectures............................................................................................................JPP 1-16
Abstracts for Oral and Poster Presentation............................................................................................................................JPP 17-88
PART B: SPECIAL ISSUE ARTICLES
Gamma Rays Induced Protein Variations in M Generation of Black Gram (Vigna mungo L.).....................................177-182
4
Varun Kaura, Bhupinder Singh, Prashant Mohanpuria,
Ranjit Kaur Gill and Navraj Kaur Sarao
Structure Modeling and Characterization of a Rhamnogalacturonan lyase......................................................................183-194
(CtRGL) from Clostridium thermocellum
Arun Dhillon and Arun Goyal
Understanding Structural Basis for Redox Regulation of Peroxiredoxin 6 using in silico approach...........................195-204
Rimpy Kaur Chowhan, Upendra Bhele, Hamidur Rahaman, and
Laishram Rajendrakumar Singh
Thermodynamics of Protein-Ligand Interactions and their Analysis.................................................................................205-217
Rummi Devi Saini
GENERAL INFORMATION, GUIDELINES AND POLICIES
The Journal: Journal of Proteins and Proteomics (JPP), administered by Proteomics Society, India
(PSI), is a peer reviewed international journal envisaged to serve the world wide community of
researchers and teachers dealing with the challenges of proteins and proteomics research resulting
in an improved understanding of protein science in general. Published quarterly, the aim is also to
supplement the regular issues with special issues annually in selected, relevant topics of protein
science. The journal has an online presence at http://www.jpp.org.in. The journal publishes wide
array of articles at no cost, whatsoever, to authors and provides free access to all articles through its
website. Hard copies of the journal are available at nominal subscription charges.
Copyright: Journal Articles by JPP is licensed under a Creative Commons Attribution-ShareAlike
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EDITORIAL NOTE : WELCOME TO THE TWENTY SIXTH ISSUE
It is a pleasure to publish the 26th issue of the journal with focuses on an area of life sciences research that
has captivated my own research interests for the last several years – protein structure, function and
dynamics. In the formative years, insight into the relationship of protein structure and dynamics with
function was also the major emphasis of the journal, which over time expanded to include all facets of
protein based research including proteomics. Jamia Millia Islamia, where research on protein folding
historically flourished, played a significant role in catapulting the journal to the national level. It was in
a conference in this centre of learning that the journal’s first special issue was published in 2012 and the
journal announced its presence on a large canvas with an objective to serving the scientific community.
The institute subsequently supported two more issues of the journal. It is thus significant that yet another
special issue of the journal is being published with the benevolence of this National University. The
special issue will be released during the National Conference on “Protein Structure and Dynamics in
Health and Agriculture”, to be held on Nov 3-4, 2017 in Jamia Millia Islamia, New Delhi, India, being
jointly organized by the Department of Biosciences and Centre for Interdisciplinary Research in Basic
Sciences.
The issue assumes even greater significance since it is also being supported by Protein Society of
India, a nascent society whose prime objective is to foster research in Protein Science. The society started
its journey in September 2015 and this happens to be the first annual meeting at the national level. What
started as informal meetings between researchers of about a dozen laboratories in New Delhi, whereby
young researchers were allowed to present and discuss their research findings in a unique setting that
nurtured their scientific dreams, morphed into a society with the prime emphasis to catalyze research
and knowledge dissemination.
This issue carries four articles. The first of these is a research communication that highlights the use
of dose-specific gamma rays to induce variations in proteins in M-4 generation of a specific plant (black
gram). The second and third research articles reports structural investigations of enzymes from bacteria
and humans. The second article reports the structure modeling and characterization of a
rhamnogalacturonylase from Clostridium thermocellum, which is an anaerobic thermophilic bacterium
that has attracted researchers due to its cellulolytic and ethanologenic abilities. It is capable of converting
a cellulosic substrate into ethanol and has commercial value. The third article tries to understand the
structural basis of redox regulation of peroxiredoxin 6, which belongs to a family of antioxidant enzymes.
This family of enzymes helps cells combat oxidative stress. Such an insight would help better
understanding of diseases that render cellular defense mechanism ineffective. The fourth article is a
review that outlines the various aspects and methods that are frequently applied to probe and analyze
thermodynamics of protein-ligand interactions. This is a simplistic outline meant to provide an initiation
into this vast and significant area of protein science research for undergraduate and postgraduate students.
In addition, the issue doubles up as Conference proceedings. It carries all the abstracts of the keynote
and plenary lectures, invited talks, oral presentations by student as well as those of the poster presentations.
The abstracts provide a quick bird’s eye view of the length and breadth of the work currently being
pursued in the area of protein science in the country and acts as a catalogue of the various topics that has
gained attention of the researchers of late.
We take the opportunity to thank the organizers of the conference for their vision and able support.
We thank the sponsors who supported associated costs through advertisements that help the journal to
be freely accessible and publish articles without any charge to authors. We thank all the executive members
of the Protein Society for their help and co-operation. We thank Proteomics Society, India (PSI) and the
members of the editorial board for supporting and administering the journal. PSI deserves special
appreciation for allowing Protein Society to be a part of the journal for this special issue. I believe that
Proteomics Society and Protein Society must work closely as a unit for greater good and together support
the journal as a scientific platform for the research community. Journal of Proteins and Proteomics (JPP)
may help forge the association.
We also thank the authors of the articles for their immense contribution. We thank all the participants
of the conference for their abstract submission in time. We indeed thank Dr. Imtaiyaz Hassan for his
priceless help with the conference proceedings as well as all aspects of the conference organization. We
also thank Prof. M. Moshahid Alam Rizvi for organizing the conference and for supporting the society
and the journal with his vision. The journal is indebted to Jamia Millia Islamia for their unconditional
support and encouragement.
We hope you will appreciate our efforts and provide us with suggestions for improvement.
Constructive criticism, suggestions and help of any kind, as always, are most welcome.
Editor in Chief
Dr. Suman Kundu
National Conference on
Protein Structure and Dynamics in Health and Agriculture
3 – 4 November, 2017
Organized by
Department of Biosciences &
Centre for Interdisciplinary Research in Basic Sciences
Jamia Millia Islamia University, Jamia Nagar, New Delhi 110025, India
Conference Venue: M.A. Ansari Auditorium, Jamia Millia Islamia University
Local Organizing Committee
Patron: Prof. Talat Ahmad
FNA; FASc; FNASc, J.C. Bose National Fellow
Vice-Chancellor
Co-Patron: Prof. Sharif Ahmad
Dean, Faculty of Natural Science
Prof. M. A. Rizwi, Chairman Dr. Md. Imtaiyaz Hassan, Convener
Dr. Asimul Islam, Co-convener Mohd. Mohsin, Treasurer
Local Committee
Arif Ali Shafeeque Ahmed Ansari Jawaid Ahmad Khan
Faizan Ahmad Luqman Ahmad Khan Sher Ali
Mohamad Aman Jairajpuri Zubaida Ansari Qazi Mohd. Rizwanul Haque
Fareeda Athar Seemi Farhat Basir Rajan Patel
Syed Akhtar Husain S. N. Kazim Tasneem Fatma
Shama Parveen Meryam Sardar Zahid Ashraf
Mohd. Abid Sonu C. Thakur Amit Kumar Verma
Romana Ishrat Nida Jamil Khan Ravins
Nadeem Ahmad Najmul Arfeen Mahfoozur Rahman
National Advisory Committee
T. P. Singh Jayant B. Udgaonkar Seyed E. Hasnain
K. V. R. Chary G. Krishnamurthy M. R. N. Murthy
Dinakar M. Salunke Alok Bhattacharya Rajiv Bhatt
P. Guptasarma Dhananjay Bhattacharya Yogendra Sharma
Punit Kaur R. Shankaranarayanan B. Jayaram
N. R. Jagannathan Pawan Sharma Amit Dutt
A. Shariff N. K. Chaudhary A. K. Singh
A. K. Mondal A. P. Singh Altaf Ahmed
Masood Ahmad A. B. Pant
Protein Society Executive Committee
Apurba K. Sau, NII (President) Pramit Kumar Chowdhury, IITD
Suman Kundu, DU (Vice President) Bishwajit Kundu, IITD
Md. Imtaiyaz Hassan, JMI (Secretary) Monica Sundd, NII
Shashank Deep, IITD (Joint Secretary) Arockiasamy Aralandu, ICGEB
Samudrala Gourinath, JNU (Joint Secretary) Ashok Kumar Patel, IITD
Neel Sarovar Bhavesh, ICGEB, (Treasurer) Rohini Muthuswami, JNU
Tapan Kumar Chaudhuri, IITD Sneha Sudha Komath, JNU
Bichitra K. Biswal, NII
JAMIA MILLIA ISLMIA
Jamia Millia Islamia came into existence in 1920 through the tireless efforts of its founders, such as Shaikhul Hind Maulana Mahmud Hasan, Maulana
Muhammad Ali Jauhar, Hakim Ajmal Khan, Dr. Mukhtar Ahmad Ansari, Jenab Abdul Majeed Khwaja and Dr. Zakir Husain. It symbolizes the unflinching
and resolute commitment of these great visionaries in bringing about socio-economic transformation of common masses, in general, and Muslims, in
particular through the vehicle of education.
While the University has come a long way since its inception, it has to keep pace with the changing needs and expectations of the society. It has to
successfully perform the multiple roles of creating new knowledge, acquiring new capabilities and producing an intelligent human resource pool for the
promotion of economic growth, cultural development, social cohesion, equity and justice.
In view of special status of Jamia Millia Islamia in our country, we need to deliberate upon reconstituting the academic programmes through introduction of
Choice-based Credit System, discuss suitable examination and administrative reforms and consider use of international benchmarks, such as Citation
index, Journal Impact factor etc. for evaluating the quality of our research. I also exhort all the faculty members to formulate research project proposals
either singly or in collaboration with other researchers of this or other institutions for financial support by the national and international funding agencies.
Apart from strengthening the teaching-learning process, research and extension programmes, special focus on extracurricular, sports and other similar
activities to foster global competencies among the students is our priority.
DEPARTMENT OF BIOSCIENCES
Department of Biosciences at Jamia Millia Islamia was established in 1985 with an aim to impart teaching with strong component of physical sciences
and, research in interdisciplinary areas of Modern Biology. In this pursuit, we also maintain in-house expertise in Pure and interface Physics, Chemistry
and Mathematics.
Our undergraduate teaching programme is radically different from other Indian universities in that it incorporates Physics, Chemistry, Mathematics on
equal footing with modern and classical biosciences. Post Graduate teaching programme of MSc-Biosciences captures entire spread of life science.
Both programmes strive to build seamless connectivity and synergy between Physical and Biological Sciences. Numerous students of ours have found
placement as teachers and researchers in all leading institutes of India and abroad.
In addition to well equipped teaching and research laboratories, the Department maintains Plant tissue culture & Green House facility, Animal, Algal,
Fungal and Bacterial cell culture facilities, High Speed Internet, Computational Facility and a Central Instrumentation Facility with trained staff which
houses equipments as Ultra-Centrifuge, A range of High Speed Centrifuges, HPLC, Stopped flow apparatus, Spectrophotometers, Spectrofluorometer,
Microplate readers, a large range of shakers and sonicators, Water purification systems, Light, Inverted & Fluorescence Microscopes, Gel Documentation
systems, PCRs, Ultra Low Temperature Freezers, Organ Bath System. These facilities complement project support mobilized from external funding
agencies like UGC, CSIR, DST, DBT, ICMR, MoEF, etc., and underpin research in a range of biological processes from Plant molecular biology,
biochemistry and virology through Protein Chemistry, Structural biology, Bioinformatics, Environmental Biology, Cancer and Cardiovascular biology, to
Algal, Fungal and Bacterial biochemistry and genetics.
Department of Biosciences is supported by DST-FIST programme as also by UGC-Special Assistance Programme.
CENTRE FOR INTERDISCIPLINARY RESEARCH IN BASIC SCIENCES
The Centre for Interdisciplinary Research in Basic Sciences was established in the year 2006. The reason for its establishment was a realization of the
fact that each modern development in biology has its roots in basic sciences. In order to achieve its goal the Centre has both basic scientists and life
scientists as faculty members who are doing research in modern areas of life sciences. There are 14 faculty members; a few of them have received
significant professional recognitions. Being an interdisciplinary research centre our faculty members are divided into self-selected research programmes
in thrust areas such as Protein Folding Problem, Structure Biology, Systems Biology, Bioinformatics, Nano-biotechnology, Bioimaging using SPM,
Medicinal Chemistry, Molecular Biology, Virology, and Molecular Reproduction Biology. The size of our research programme allows the Centre to
provide challenging research experiences to our students and researchers. The Centre offers two semesters extensive pre-Ph D course of 24 credits
(16 credits of theory courses and 8 credits of practical courses). The purpose of this course is to prepare basic scientists (M.Sc. in chemistry/ physics/
mathematics/ computer science), and life scientists (M.Sc. in all branches of biology) to pursue interdisciplinary research in the novel areas of biological
sciences. This is achieved by introducing courses from life sciences to basic scientists and courses from basic sciences to life scientists during their
pre-Ph.D. course work. This is a unique feature of the Centre, which is available only in a few Indian universities.
We make every effort to integrate our educational programmes into research programmes for both graduate and post-graduate students. The research
experience of our faculty members is brought to the classroom, giving students a sense of the excitement and the cutting edge nature of the discipline. In
addition, the Centre is committed to provide short term (3 months) and long term (6 months) research trainings to national and international students and
research facilities to researchers who are deprived of such facilities for extended periods. The research grants brought by our faculty members are important
in supporting research and training programmes of the Centre. As a whole, the faculty members are pursuing major research projects worth 5 crores funded
by various national and international funding agencies and have published more than 150 papers in peer reviewed journals in the last three years.
The objectives of the Centre are
• To promote interdisciplinary scientific research, advanced teaching and training in chosen areas of interdisciplinary basic sciences leading to M.
Phil and PhD degrees;
• To provide a forum for interaction among scientists, research workers, teachers and students with national and international experts;
• To provide research facilities to individual workers or research groups, especially to those who are deprived of such facilities for extended periods;
• To create tenure-based short term and long term chairs and visiting positions for experts in identified areas for interaction with the Centers’ faculty,
carrying out research and exchange of ideas; and
• To conduct seminars, workshops, conferences and extension lectures to promote interdisciplinary research in basic sciences.

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It is indeed a matter of great pleasure that the Department of Biosciences and Centre for Interdisciplinary
Research in Basic Science are jointly organising a “National Conference on Protein Structure and Dynamics
in Health and Agriculture” along with the Protein Society as its primary endeavour during November 3-
4, 2017 in the Jamia Millia Islamia. This is highly satisfactory to note that this conference is unique in its
approach as it is first joint venture between the Department of Biosciences and Centre for Interdisciplinary
Research in Basic Science. For this, I wish to give full credit to our visionary vice chancellor Prof. Talat
Ahmad for his encouraging approach towards the philosophy of promotion of interdepartmental
association. One of the purposes of this conference is to let our young scientists and budding research
students of different disciplines, know how the knowledge of protein structure is useful to provide answers
to a plethora of biological problems. This purpose shall be fulfilled by inviting the galaxy of eminent
scientists, doing research in the various frontiers of the health and agricultural proteomics and related
areas, for their talks and interactions. The diasporas is likely to cover major areas, including Protein
folding, Aggregation and Diseases, Protein structure, Dynamics and Function, Microbial proteins,
Molecular and Genetic pathogenesis, in addition to the cutting-edge methods in structural biology. The
conference shall provide opportunities of networking and scientific collaborations through audience
discussions, poster presentations, sponsored exhibitions evening ceremonies and receptions.
All work embodied in the ‘Abstract Book’ will be presented orally or through posters. Indeed it is a great
solace for the participant that all abstracts have been published in a special issue of the Journal of Protein
and Proteomics. The conference shall offer for the first time, best presentation award named on Prof.
M. Amin, the founder of the Department of Biosciences, JMI and a reputed Biophysical Scientist.
I am confident that your participation will be fruitful and your stay at the Jamia Millia Islamia during the
conference will be meaningful.
Prof. M. Moshahid Alam Rizvi
Chairman of Conference