S-S Bond in Proteins

S-S Bond in Proteins

Disulfide bond also known as S-S bond, or sometimes disulfide bridge. It is a covalent bond derived from two thiol groups. More importantly, these bonds observed to play an important role in protein stability and aggregation of large biomolecules.

SS bonds are formed by a thiol/disulfide exchange reaction, and three important factors are required in the reactive groups to form this bond: accessibility, proximity, and reactivity (electrostatic environment).


The most common way of creating this bond is by the oxidation of sulfhydryl groups. (2 RSH → RS-SR + 2 H+ + 2 e-) This process of oxidation can produce stable protein dimers, polymers, or complexes, in which the sulfide bonds can help in protein folding.


Disulfide bonds can occur two ways:

·         Intramolecularly – occurs within a polypeptide chain and are usually responsible for stabilizing tertiary structures of proteins.

·         Intermolecularly- occurs between polypeptide chains and are attributed to stabilizing quaternary protein structures.






Following Image credit goes to Wikipedia and Maria Monica Castellanos and Coray M. Colina of Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States

Some Useful tips !

Some Useful tips !

Personal Statement Guidelines

Personal statement is simply a collection of your strengths which try to show about your achievements and share your career aspirations. There is no hard and fast rule but principally, your personal statement should be a small and concise,your professionalism, and what you have to offer in terms of academic experience and ambition


Important questions that should be addressed in your personal statement:

What are your reasons for wanting to study PhD physics?
Why are you  interested in studying physics at ……….(name of university)  versus another university?
What are your long-term goals as a Physicist/Scientist?
What personal or academic characteristics are unique about you than others?
What are your personal interests?
What are your research experiences?

In the end, it needs to Include information about your college or University and the faculty writing your recommendations…


Follow the suggestions from the experts: words copied from https://www.theguardian.com

By all means mention what hooked you in the beginning, but do also mention what you are doing now to deepen your understanding,” says Anton Machacek, a physics teacher who graduated from Trinity College, Oxford.

He said “Popular science programmes rarely develop your thinking skills in the way universities will want. In this sense, I would say that the influence of Nina and her Nefarious Neurons on you as a toddler might count more in your favour than Prof Brian Cox at age 16.”

Think about which skills are relevant to your application: for example, computing experience will help you with a theoretical physics degree.

Machacek says it’s a shame that students often forget to talk about their A-level courses in their personal statements. “It’s no good saying ‘I’ve studied A-level physics’ – they already know that,” he says. “But you can say what skills you enjoyed developing and which areas excited you.”


Be specific. If The Big Bang Theory sparked your interest in physics, explain why. Schomerus, for instance, likes the episode where Sheldon takes a job as an unpaid waiter to try to discover how electrons move through graphene – it’s an area he’s done research in.

Make the statement truly personal,” he says, a point reiterated by Machacek, who is also a visiting research scientist at the Central Laser Facility in Rutherford.

“It is extremely important to be yourself,” he says. “If you are a quiet, modest type, and you force yourself to write an extrovert’s personal statement to make you seem bigger, very odd things can happen if you are interviewed.”

Most admissions tutors advise that content should always trump style or creativity, but stress that writing should be coherent because physicists must be able to communicate.


Extra-curricular activities can reflect passion – working at a science museum, being a member of a local astronomy society or having visited Cern, for example – but tutors realise that not everybody has these opportunities. Simply making the most of your school’s library is fine if it gives you a deeper appreciation of physics.

Some medications and its effect on Human Kidney (Renal System)

Some medications and its effect on Human Kidney (Renal System)

Several research findings reveals that some medications are harmful for Kidney function and responsible for Kidney stone formation.


“Medications that can damage the kidneys are known as “nephrotoxic medications.”

  • As we know whenever we go to the hospital having health issues, our treatment generally starts with antibiotic prescriptions. The problem arises when some of these antibiotics help to make crystals in renal system which don’t break down and blocks urinary track and hence urine flow.


  • Also, antibiotics constitutes some substances that can damage certain kidney cells when they try to filter them out. Some people also have allergic reactions to antibiotics that can affect their kidneys. All these things are more likely to happen if you take antibiotics for a long time or very high dose.

Vancomycin is an antibiotic used to treat severe  infections (methicillin-resistant Staphylococcus aureus (MRSA)) but research found  it cause kidney  damage and acute interstitial nephritis, or swelling in the kidney.”

     “Aminoglycoside Antibiotics are known for causing kidney injury (nephrotoxicity), even at low doses. People with chronic kidney disease, dehydration, or those who have been taking these antibiotics for a long time are at particularly high risk. The most toxic aminoglycoside is neomycin. Although these medications are typically intravenous and used in hospitals, they are important to keep at the back of your mind”


  • Water pills are used to treat high blood pressure and some kinds of swelling. They help our body get rid of extra fluid. But they can sometimes dehydrate or lowers the water level of our body, which can be bad for our kidneys.

  • Non-Steroidal Anti-Inflammatory Drugs (NSAIDs)  like aspirin, ibuprofen, or naproxen  shouldn’t use them regularly for a long time or take high doses of them.

  • Some medications like omeprazole, Aciphex, Prilosec, Prevacid, Nexium are used to treat heartburn, ulcers, and acid reflux also called Proton Pump Inhibitors (PPIs).These drugs principally works by blocking the secretion of gastric acid. Although these powerful acid blockers were never designed for long-term use but unfortunately millions of peoples around the globe take these drugs indefinitely which potentially cause deadly consequences They lower the amount of acid in our stomach, but recent studies have shown that taking them for a long time can raise our chances of serious kidney problems and possibly lead to kidney failure. Researcher suggested that If you take a PPI regularly, ask your doctor about the possibility of switching to another drug which might  be far better for your health .Now, a new study from Stanford University shows these drugs double the risk of dying from a heart attack or stroke.

  • Some supplements like creatine and wormwood oil, may bad for our kidneys. It is recommended to tell your doctor about every supplement you take to make sure they’re helping or leading to damage of your body organ.

Important Secondary Structure in Protein: α-Helices and β-Sheets

Important Secondary Structure in Protein: α-Helices and β-Sheets


One of the most common type of secondary structure found in proteins is the α-helix. Existence of  this type of structure was first predicted by Linus Pauling. Linus Carl Pauling was an American chemist, biochemist, peace activist, author, educator, and husband of American human rights activist Ava Helen Pauling.

But after several years of his prediction and was confirmed when the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew) was determined by X-ray crystallography.

To give you a better impression of how a helix looks like, only the main chain of the polypeptide (a linear organic polymer consisting of a large number of amino-acid residues bonded together in a chain, forming part of (or the whole of) a protein molecule)  is show in the figure, no side chains. There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). Each residue is translated 1.5 Å along the helix axis, which gives a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). The α-helix is the major structural element in proteins.

An example of an α-helix is shown on the figure below, such type of representation of a protein structure is called sticks representation.

In figure-2, When looking at the helix in the figure below, we notice how the carbonyl oxygen atoms C=O (shown in red) point in one direction, towards the amide NH groups 4 residues away (i, i+4). Together these groups form a hydrogen bond, one of the main forces in the stabilization of secondary structure in proteins. The hydrogen bonds are shown on the right figure as dashed lines. It is found that most of the alpha helices in protein are right handed




The second major type of secondary structure in proteins is the β-sheet. β-sheets consist of several β-strands, stretched segments of the polypeptide chain kept together by a network of hydrogen bonds.he β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands (also β-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimer’s disease.

An example of a β-sheet with the stabilizing hydrogen bonds shown as dashed lines is shown on the figure below:

The figure shows how hydrogen bonds link different segments of the polypeptide chain. These segments do not need to follow to each other in the sequence and may be located in different regions of the polypeptide chain.

The same β-sheet is shown on the figure below, this time in the context of the 3D structure to which it belongs and in a so-called “ribbon” representation (the coloring here is according to secondary structure – β-sheets in yellow and helices in magenta). In the figure each β−strand is represented by an arrow, which defines its direction starting from the N-terminus to the C-terminus. When the strand arrows point in the same direction, we call such β-sheet parallel:


When the strand arrows point in opposite directions, the sheet is anti-parallel. In the next figure you can see an example of a protein structure with an anti-parallel β-sheet:


Visual Molecular Dynamic (VMD)  Study of Large structure Biomolecules !

Visual Molecular Dynamic (VMD) Study of Large structure Biomolecules !

Nowadays, it is noticed that the research trend is looping towards  interdisciplinary approach like  Connecting Physical dynamics to biological structure and their data obtained from diverse experimental sources for example molecular dynamics simulations helps to explore and study of biological phenomena in unparalleled fashion.
With necessary updates on simulations techniques leading towards the high resolution (up to atomic level)  descriptions of biological molecules/systems into the million-to-billion atom regime, in which numerous cell functions reside.

 In this process, we review the trajectory of the entire process, driven by simple law of motion (F=ma) of large-scale molecular dynamics  simulations.

                                                                        Fig: VMD Image of Human Serum Albumin

                      So, new research finds says about utility of molecular dynamics simulations in the critical task of relating atomic level detail to the function of large structure molecular complexes which is a task that cannot be simply achieved by smaller-scale simulations or existing experimental approaches used before.

Exclusive interview with Prof. Lawerence M. Krauss, Arizona State University | Chetanath Blog

Exclusive interview with Prof. Lawerence M. Krauss, Arizona State University | Chetanath Blog

This is Chetanath Neupane,
Editor, New Dimension Magazine
Department of Physics, St. Xavier’s College, Kathmandu, Nepal.

Professor Lawrence M. Krauss, thank you very much for providing your precious time for our magazine. Personally I am very happy and much eager to talk to the best-selling author of several books and more than 300 research publications & Director, The Origins Project at ASU and Foundation Professor, School of Earth & Space Exploration and Physics Department Arizona State University. I would like to welcome you to this session On New Dimension Magazine.

  • Professor Krauss, you are very busy person. How do you manage your time?

I try and agree to do many different things, and then juggle them one at a time. I find that if I don’t have a lot to do, I sometimes do very little. I tend to focus intensively on one thing at a time, and work through the list. Sometimes I have to focus on 3 or 4 very different things in a single day, but I actually like the variety as well.

  • Dear Professor, first of all I would like to Congratulate for your recent book publication “The Greatest Story Ever Told…So Far” , how do you introduce this book to laymen what is the greatest story in this book?

“It is the story of the remarkable effort humans have made to understand the fundamental forces that govern nature, and to strip back the illusion of reality that we experience on human scales to understand the underlying structure beneath it.”

  • It is said that life in the Universe can occur only when certain universal dimensionless physical constants lie within a very narrow range. In what sense, if any, is the universe fine-tuned? What conclusions should we draw from the existence of fine-tuning?

“The Universe isn’t fine tuned for life. Life is fine-tuned for the universe. If the parameters of the universe were different perhaps different life forms might be possible. Moreover, even quantities like the energy of empty space, which seems to be so small compared to the value it might have, and which, if it were any larger, would not allow galaxies to have formed, could nevertheless have been much smaller and the universe would be more conducive to life. And a value of zero for this quantity would seem very natural indeed.”

  • Prof. Krauss, I kindly expect your answer in my personal question arising while going through your another famous book “A Universe from Nothing” which contains an argument, why there is something rather than nothing. How can you explain it to a non-physicist, how the universe can be created out of nothing?

“Well, quantum mechanics allows for the spontaneous emission of particles like photons, the particles that make up light, whenever an electron changes its state in an atom. The photon appears from nothing. It was not in the atom before it was emitted. It simply appeared. Similarly, it turns out that elementary particles can spontaneously appear in empty space, once again due to the properties of quantum mechanics, this time in combination with relativity. If gravity is a quantum theory, then the variables that gravity describes, space and time, become quantum mechanical in nature, and whole space-times can appear spontaneously. This means that whole universes can appear that did not exist before. And it turns out our universe has the properties that one would expect from a universe that spontaneously appeared from nothing in this way.”

  • Do you agree that “philosophy” is the best way to understand Physics and Nature?

“Natural-Philosophy, what we now call Science is the best, and I believe, the only reliable way to understand how the physical universe operates.”

  • If time (or space) is infinite, everything that can happen has already happened, even down to me typing these words, and there is no change, only cycles of varying lengths. But how could time not be infinite? How can there be no state of being at all?

“Our universe had, as far as we can tell, a beginning, about 13.8 billion years ago. As far as we can tell, both space and time may have begun then. Now, as far as we can tell, our universe may expand forever. So in that sense time could be infinite..(or as we say in physics or mathematics, semi-infinite). And it is true that if our universe exists into the indefinite future then many strange aspects of infinity, including the possible repetition of everything we experience, an infinite number of times, for separate versions of us, might be possible. But we certainly don’t know if this is the case, and the conditions of the future universe could change so that life forms like us could not exist in the far future in any case.”

  • Once you have said “String theory doesn’t really make any predictions at this point because it’s still an evolving idea”, is there any significant development in this idea?

“There has been a lot of mathematical development, and interest techniques have been developed that have been useful in other areas of physics. But fundamentally my earlier statement remains the same.”

  • You say that you are an atheist. How do you define atheism? Are you an atheist because of your scientific consciousness?

“An atheist is simply someone who finds the argument for God unconvincing. Everything I have learned as a scientist over the past 35 years makes God not only seems highly unlikely, but largely redundant even if such an entity did exist. There is no evidence for miracles, and the laws of physics describe the history of the universe back to the earliest moments of the big bang without supernatural shenanigans.”

  • Professor, Is “Dishonest” the only word for someone who believes in god despite being a scientist?

“No, I don’t think so. A vague ‘deist’ notion.. Assuming some purpose or order in the universe determined by some unknown intelligence, cannot be refuted by science. It is just unnecessary. But the Gods of the world’s major religions are all not in accord with our scientific understanding of nature. I wouldn’t call it dishonesty. Religion is foisted on young people, and it is hard to overcome.. We all tend to believe in mutually contradictory things at one time or another.”

  • Professor, let we discuss about the global scenario, In January 2017, the Doomsday Clock is set at two and a half minutes to midnight, due to a rise of strident nationalism worldwide, US President Donald Trump’s comments over North Korea, Russia, nuclear weapons, and the disbelief in the scientific consensus over climate change by the Trump Administration. What is the real picture of our planet at this point? Are we heading towards world war III?

“Who knows? The world is a dangerous place, and we have to wake up to those dangers and begin to think globally. As Einstein said many years ago after the first nuclear explosion, “Everything has changed, save the way we think”. Unfortunately our thinking remains the same.”

  • In the end, What is your message to young researcher in Nepal?

“Keep doing what you love. Don’t get discouraged by others. Work hard, and enjoy discussing your work with others. .”

For more about Prof. Krauss go through the following Links:

Physics behind OM mantra | Quanta-Aum

Physics behind OM mantra | Quanta-Aum

Physicists believe a cubic centimeter of empty space may contain enough quantum energy to run our entire planet. Science is just at beginning to learn how to tap into this fundamental life force to expand consciousness and heal our bodies. It is widely accepted that yoga, meditation and other practices that involve conscious relaxation can reduce stress and enhance a person’s general well-being. Researcher at Massachusetts General Hospital and Beth Israel Deaconess Medical Centre report that the relaxation response a state of deep rest attained through breathing, meditation, yoga and other practices triggers changes in gene expression that can affect the body’s immune function, energy metabolism and insulin secretion. Meditation is very essential for human beings to come out of the different troubles. OM or AUM is a spiritual mantra, important to obtain peace and calm. The entire mental pressure has been taken away by chanting OM mantra. Consciousness has been improved by the reception of OM mantra. The time-frequency analysis has been decided that the OM chanting affords steadiness in the mind scientifically. The mental stress of a person gets reduced while the mind reaches steadiness. The visual elements of the OM symbol represent the four states of consciousness (1-4), and the world of illusion (5):

  • Walking (jagrat) – 1
  • Dreaming (swapna)— 2
  • Deep sleep (sushupti)— 3
  • Transcendental state (turiya) –4
  • World of illusion (maya) – 5

The dot (indicated by 4) signifies the fourth state of consciousness, known in Sanskrit as turiya. In this state the consciousness looks neither outwards nor inwards (it is known as no divergence in physics), nor the two together (Pauli exclusion principle for electron occupancy).

The upper curve (indicated by 3) denotes the state of deep sleep (sushupti) or the unconscious state. This is a state where the sleeper desires nothing beholds any dream (bounded system in physics).

The larger lower curve (indicated by 1) symbolizes the waking state (jagrat), in this state the consciousness is turned outwards through the gates of the senses. The larger size signifies that this is most common or majority state (similar to overlap integral concept in quantum mechanics) of the human consciousness.

The semi-circle (indicated by 5) symbolizes maya and separates the dot from other three curves. Thus it is the illusion of maya that prevents us from the realization of this highest state of bliss. The semi-circle is open at the top and does not touch the dot. This means that this highest state is not affected by maya. Maya only affects the manifested phenomenon. (like derivative of constant times variable term like ‘2x’affects only to variable not to constant).

The middle curve signifies the dream state (swapna) which lies between deep sleep and the waking state. (singularity state beyond time and space, in which time and space are embedded, without contradiction or simply like a complex formation reaction in chemistry). In this state the consciousness of the individual is turned inwards and the dreaming self-beholds an enthralling view of the world behind the lids of the eyes.

Imagine that the ultimate smallest subatomic particles are nothing but God itself appearing to be a multitude to an outside observer, but in reality a homogeneity and continuum of one and the same substance. Let’s call these as quanta of God, imagine that depending on the ways of these quanta are configured in the relative world with respect to each other that they can cancel each other’s effect resulting in inertia or interact so as to generate a movement, a strongly spinning vertex which we observe as material particles or reinforce each other in a resonance superposition, bringing forth the harmonic OM-vector. Once OM vector is established it can never disappear, it can only grow and acts as organizing intelligent principle that leads to that configuration of matter we call life. Moreover, this vector can bind and organize matter at the higher aggregation level of atoms, molecules etc.

Figure source: www.google.com

Hence, from above we can say that the all the material/substances can be obtained from OM vector. From OM vector we can derive all the laws of fundamental sciences taking them as a special case in the solution of God’s harmonic equation containing OM vector.